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Multiple start and stop codons in mRNA and pre-mRNA

Multiple start and stop codons in mRNA and pre-mRNA


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I have a main question that will lead to further questions depending upon the answer.

In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA? If there is, do they remain in the mRNA after splicing? If they do, does that mean one mRNA has the coding sequence for the synthesis of multiple different proteins?

One last question: assuming a single mRNA has the sequence for synthesis of a single protein, is the stop codon always the final sequence before the poly-A tail?

Thanks in advance for your help and sorry for the mini rabbit hole.


Whether or not there are multiple start and stop codons depends on what you mean by "start codon" and "stop codon".

The start codon has the sequence "AUG", and the stop codon has the sequence "UAG", "UAA", or "UGA". Both the pre-mRNA and the mature-mRNA can, and usually do, contain multiple instances of all of these sequences. However, only one "AUG" instance serves as the translational start site, and only one instance of the stop codon sequence serves as the translational stop site.

The translational start site is usually the first (5' most) AUG. However, for reasons that are still not entirely understood, in about 5% of genes the first AUG is skipped, and translation starts at one of the other AUG sequences.

The translational stop site is always the first stop codon to occur in-frame with the translational start site in the mature mRNA.

The stop codon is usually not (I'm tempted to say never) the final sequence before the poly-A-tail. The coding sequence (the RNA region that codes for the protein) occurs in the middle. There is a 5' untranslated region (UTR) before the protein coding region, and a 3' UTR after the protein coding region. The UTR sequences vary among genes and can have different functions depending on the sequence.


As this question is a first post it is probably just a basic question about protein synthesis, which @Sean Johnson has answered adequately. However I'm not quite sure. And as I used to work in protein synthesis (but am a rather out of touch now) I decided to look at the recent literature a little to address some more esoteric or obscure questions it raised in my mind. I've set out the results below, and divided my answer into mature mRNA (which Sean covered primarily) but have also considered pre-mRNA. If the answer is not very useful to the questioner it may still be of interest to others.

Start and Stop Codons in Mature mRNA

The general picture of initiation and termination of protein biosynthesis in eukaryotes (bacteria and archea are different) has been described by Sean and can be found in standard texts1. In most cases the first AUG from the 5'-end of the mRNA is the one recognized as the 'start' signal for protein synthesis by the ribosomal-subunit initiation complex that scans along from the cap, according to the Kozak model2; and any one of the three termination codons encountered in the reading frame is recognized as 'stop' and (almost) invariably lead to termination of the polypeptide chain.

START EXCEPTION 1
As mentioned, in some 5% of mRNAs certain aspects of the environment of the first AUG from the 5'-end results in it being ignored by the complex, and the insertion of methionine and start protein synthesis occurs at the second (or perhaps even a subsequent) AUG.2

START EXCEPTION 2
Certain eukaryotic viruses were found to initiate the translation of the mRNAs internally, by a mechanism distinct from the 5'-scanning method. This involves an 'internal ribosomal entry site' - IRES. It subsequently transpired that a small subset of host mRNAs posses an IRES and can initiate translation internally. These include some growth factors, transcription factors and translation factors.3 Such (rare) mRNAs can therefore have several AUGs in their 5'-untranslated region.

Although it is possible to envisage an mRNA with several IRESs, and thus encoding several different proteins (analogous to a bacterial polycistronic mRNA), this does not appear to happen. It is striking, for example, that poliovirus RNA has just a single IRES for the start of the synthesis of single a large polyprotein, from which it generates multiple proteins by proteolysis. It would seem that the main purpose of this alternative initiation is to allow protein synthesis to proceed in the absence of a 5'-cap.

STOP EXCEPTION 1
There are some AGU codons that are recognized by a specific tRNA that inserts selenocysteine into the polypeptide chain. Some aspect of the environment of these codons causes them to be ignored by the protein termination system, and the ribosome continues translating, eventually terminating at a subsequent stop codon4.

STOP EXCEPTION 2
It has long been known that certain bacterial and eukaryotic viral mRNAs can increase their genetic repertoire by what is known as 'read-through' of 'leaky' stop codons. This is a 'percentage' effect, rather than all or nothing, and results in a mixture of 'normal-length' and extended products. It is now clear that the same phenomenon can occur in some eukaryotic mRNAs: quite frequently in Drosophila5, but also in mammals6.

STOP CODONS & THE 3'-UTR
I'm not clear what the questioner means by “is the stop codon always the final sequence before the poly-A tail?”. If the question is whether there can be additional stop codons in the 3'-UTR between the functional termination codon and the AATAAA polyadenylation signal (purple in Sean's diagram) the answer is yes. Looking at the sequences of some muscle protein cDNAs done years ago, I found several stop codons in this region in each that I looked at. Of course they are without any function as the ribosome has already departed, but there is no reason for them not to be there on a random basis (and at apparently random positions).

Start and Stop Codons in pre-mRNA

By pre-mRNA I assume is meant the initial RNA transcript before splicing. There is no reason why an intron that is spliced out so that it does not appear in the final mRNA should not contain start or stop codons, which if not removed would have altered the reading frame. Many do.

A more interesting situation is where there is alternative splicing to produce different mRNA transcripts that encode different proteins. Pertinent to the question is the situation with start codons where the proteins differ in their N-termini, and stop codons where the proteins differ in their C-termini. The latter are quite common, but the former also occur, particularly were there are alternative forms of a protein, with and without a signal peptide7. In these cases the start or stop codons will be present in both of two exons, one of which is spliced out in each case. Examples of this from a couple of Drosophila genes are illustrated:

In both cases the coding regions are in orange, and the untranslated regions in grey. The thin lines represent the position of introns that have been spliced out. The arrowhead represents the direction of transcription and is at the C-terminal side of the protein. (i) Different N-termini for alternative products of gene vha14-2; (ii) Different C-termini for alternative products of gene vhaSFD.9


Dna Replication Transcription And Translation Biology Essay

This chapter briefly outlines the concept of DNA replication and intends to make the reader understand how DNA replicates itself. The details of transcription of DNA into RNA will also be explained. Lastly, translation of RNA into proteins will be elaborated.

Most people think that these topics are in the realm of pure molecular biologist and the researcher. Unfortunately, this is not true. Before a pathologist embarks on the study of techniques used in molecular pathology, a brief outline of the basic concepts is in order.


Multiple start and stop codons in mRNA and pre-mRNA - Biology

Membrane-permeable compounds that reversibly inhibit a particular step in gene expression are highly useful tools for cell biological and biochemical/structural studies. In comparison with other gene expression steps where multiple small molecule effectors are available, very few compounds have been described that act as general inhibitors of pre-mRNA splicing. Here we report construction and validation of a set of mammalian cell lines suitable for the identification of small molecule inhibitors of pre-mRNA splicing. Using these cell lines, we identified the natural product isoginkgetin as a general inhibitor of both the major and minor spliceosomes. Isoginkgetin inhibits splicing both in vivo and in vitro at similar micromolar concentrations. It appears to do so by preventing stable recruitment of the U4/U5/U6 tri-small nuclear ribonucleoprotein, resulting in accumulation of the prespliceosomal A complex. Like two other recently reported general pre-mRNA splicing inhibitors, isoginkgetin has been previously described as an anti-tumor agent. Our results suggest that splicing inhibition is the mechanistic basis of the anti-tumor activity of isoginkgetin. Thus, pre-mRNA splicing inhibitors may represent a novel avenue for development of new anti-cancer agents.


Mitochondrial RNA editing in trypanosomes: small RNAs in control

Mitochondrial mRNA editing in trypanosomes is a posttranscriptional processing pathway thereby uridine residues (Us) are inserted into, or deleted from, messenger RNA precursors. By correcting frameshifts, introducing start and stop codons, and often adding most of the coding sequence, editing restores open reading frames for mitochondrially-encoded mRNAs. There can be hundreds of editing events in a single pre-mRNA, typically spaced by few nucleotides, with U-insertions outnumbering U-deletions by approximately 10-fold. The mitochondrial genome is composed of ∼50 maxicircles and thousands of minicircles. Catenated maxi- and minicircles are packed into a dense structure called the kinetoplast maxicircles yield rRNA and mRNA precursors while guide RNAs (gRNAs) are produced predominantly from minicircles, although varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Guide RNAs specify positions and the numbers of inserted or deleted Us by hybridizing to pre-mRNA and forming series of mismatches. These 50-60 nucleotide (nt) molecules are 3' uridylated by RET1 TUTase and stabilized via association with the gRNA binding complex (GRBC). Editing reactions of mRNA cleavage, U-insertion or deletion, and ligation are catalyzed by the RNA editing core complex (RECC). To function in mitochondrial translation, pre-mRNAs must further undergo post-editing 3' modification by polyadenylation/uridylation. Recent studies revealed a highly compound nature of mRNA editing and polyadenylation complexes and their interactions with the translational machinery. Here we focus on mechanisms of RNA editing and its functional coupling with pre- and post-editing 3' mRNA modification and gRNA maturation pathways.

Keywords: Cryptogenes Mitochondria Protein complexes RNA binding proteins RNA editing RNA ligase RNase III TUTase Trypanosoma.

Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Figures

The RNA editing core complex…

The RNA editing core complex catalyzes elementary RNA editing reactions. Direct protein-protein interactions…


How can 1 mRNA molecule have 6 reading frames?

If translation always begins at a start codon, how can an mRNA molecule have multiple reading frames? Wouldn't it only have 1 since translation has to start at the start codon? Or can an mRNA molecule have multiple start codons or something? Thanks!

You are basically correct.

6? If you have a piece of DNA, and do not know where the start is or even which strand, there are six possible reading frames -- conceptually. Two strands, 3 frames each. If you know the strand, there are 3 if you know the start codon, you got it.

(There are possible complexities about alternative start codons, but probably not relevant here.)

An mRNA molecule will only have 3 reading frames maximum (6 is for the DNA which has 2 strands).

But there is a distinction between "reading frame" and "open reading frame". For a given sequence, you have :

AUG AAA AGG
XAU GAA AGG
XXA UGA AAG

Notice how both reading frames 1 and 2 have a stop codon AGG. Stop-codons may sometimes be "hidden stops", when if you do a frameshift of one nucleotide, you make a stop codon appear. But only the reading frame 1 will give you a proper Open Reading Frame, with start and stop codon.


Sdeochand1

Everyone knows that oxygen is essential for many animals, especially humans, to survive on earth because it is necessary in order to preform certain metabolic processes. Oxygen is carried throughout our body via the protein hemoglobin, and proteins are coded from our DNA. DNA is a series of three nucleotides called a codon. Some codons are exons, coding for a protein, while others are introns, not coding for proteins. With exons and introns scattered along the chromosome, DNA has a special codon to signal the beginning of an exon: AUG. So technically, without the codon AUG, tRNA would not know where to start coding for the proteins that make up hemoglobin. While oxygen is very important, the codon AUG is more important.

When you stop to think about the whole concept of codons and how they relate to proteins, it really is mind blowing. There are only a hand full of codons that actually participate in coding for a protein. These codons are universal for all species, even bacteria. Like mentioned before, there is one start codon, AUG, that is also universal for all species that signals the start of translation. Since there are start codons, stop codons also exist to signal the end of translation.

Now stop and think about our chromosomes and how much DNA we have on those chromosomes. And to think that more than half of our DNA is basically a nonsensical pattern of codons that mean absolutely nothing. That is essentially what an intron is. The most important part of our DNA is the exon, where the genes really are stored. Those start and stop codons distinguish the difference between introns and exons. Now how are the exons separated from the introns? A special RNA called small nuclear RNA (snRNA) cuts out the introns.

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There is a little confusion in terminology. In DNA, we do not talk about codons. This is something we will only talk about with RNA. In DNA, we have genes. Genes code for some product, mainly proteins. So, in your example, there are genes on DNA that code for Hemoglobin.

Now, when you make a transcript of a gene, or mRNA, you are providing the code for how to build this protein to a ribosome (the process of translation).

When a pre-mRNA is made, we have to splice out unused information (introns), so that only the useful information (exons) remail.

Now, the process of translation is moving from the language of Nucleic Acids (sequences of nucleotides) to the language of proteins (sequences of amino acids). To do this, we need to know how to read the sequences. A sequence of 3 nucleotides represents 1 amino acid. Those three nucleotides are referred to as a codon. Starting at the Start Codon (AUG), every subsequent set of three nucleotides on mRNA is considered a codon.


Maps, Directions, and Place Reviews

The brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, an mRNA molecule may also be processed, edited, and transported prior to translation. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP.

Transcription

Transcription is when RNA is made from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process is similar in eukaryotes and prokaryotes. One notable difference, however, is that eukaryotic RNA polymerase associates with mRNA-processing enzymes during transcription so that processing can proceed quickly after the start of transcription. The short-lived, unprocessed or partially processed product is termed precursor mRNA, or pre-mRNA once completely processed, it is termed mature mRNA.

Eukaryotic pre-mRNA processing

Processing of mRNA differs greatly among eukaryotes, bacteria, and archea. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires extensive processing.

5' cap addition

A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m 7 G cap) is a modified guanine nucleotide that has been added to the "front" or 5' end of a eukaryotic messenger RNA shortly after the start of transcription. The 5' cap consists of a terminal 7-methylguanosine residue that is linked through a 5'-5'-triphosphate bond to the first transcribed nucleotide. Its presence is critical for recognition by the ribosome and protection from RNases.

Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step biochemical reaction.

Editing

In some instances, an mRNA will be edited, changing the nucleotide composition of that mRNA. An example in humans is the apolipoprotein B mRNA, which is edited in some tissues, but not others. The editing creates an early stop codon, which, upon translation, produces a shorter protein.

Polyadenylation

Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA (mRNA) molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine (oligouridylation) are also common. The poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. mRNA can also be polyadenylated in prokaryotic organisms, where poly(A) tails act to facilitate, rather than impede, exonucleolytic degradation.

Polyadenylation occurs during and/or immediately after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site. This reaction is catalyzed by polyadenylate polymerase. Just as in alternative splicing, there can be more than one polyadenylation variant of an mRNA.

Polyadenylation site mutations also occur. The primary RNA transcript of a gene is cleaved at the poly-A addition site, and 100-200 A's are added to the 3' end of the RNA. If this site is altered, an abnormally long and unstable mRNA construct will be formed.

Transport

Another difference between eukaryotes and prokaryotes is mRNA transport. Because eukaryotic transcription and translation is compartmentally separated, eukaryotic mRNAs must be exported from the nucleus to the cytoplasm--a process that may be regulated by different signaling pathways. Mature mRNAs are recognized by their processed modifications and then exported through the nuclear pore by binding to the cap-binding proteins CBP20 and CBP80, as well as the transcription/export complex (TREX). Multiple mRNA export pathways have been identified in eukaryotes.

In spatially complex cells, some mRNAs are transported to particular subcellar destinations. In mature neurons, certain mRNA are transported from the soma to dendrites. One site of mRNA translation is at polyribosomes selectively localized beneath synapses. The mRNA for Arc/Arg3.1 is induced by synaptic activity and localizes selectively near active synapses based on signals generated by NMDA receptors. Other mRNAs also move into dendrites in response to external stimuli, such as ?-actin mRNA. Upon export from the nucleus, actin mRNA associates with ZBP1 and the 40S subunit. The complex is bound by a motor protein and is transported to the target location (neurite extension) along the cytoskeleton. Eventually ZBP1 is phosphorylated by Src in order for translation to be initiated. In developing neurons, mRNAs are also transported into growing axons and especially growth cones. Many mRNAs are marked with so-called "zip codes," which target their transport to a specific location.

Translation

Because prokaryotic mRNA does not need to be processed or transported, translation by the ribosome can begin immediately after the end of transcription. Therefore, it can be said that prokaryotic translation is coupled to transcription and occurs co-transcriptionally.

Eukaryotic mRNA that has been processed and transported to the cytoplasm (i.e., mature mRNA) can then be translated by the ribosome. Translation may occur at ribosomes free-floating in the cytoplasm, or directed to the endoplasmic reticulum by the signal recognition particle. Therefore, unlike in prokaryotes, eukaryotic translation is not directly coupled to transcription.


Protein Synthesis

In essence, genetic information in DNA is accessed via a process called transcription, whereby “excerpts” of information in a DNA molecule are copied to RNA molecules. The RNA copies are sent out to be read and “acted upon” in a process called translation, whereby these excerpts of genetic information are used as blueprints for the building of proteins . Proteins are the vital “molecular tools” that will eventually carry out the cellular work that all organisms need for survival, growth, and development.

This mechanism for the flow of genetic information in organisms is known as the centraldogma of molecular biology , which states that information flows from DNA to RNA to proteins through the processes of transcription and translation. Thus, the central dogma describes the pathway from an organism’s genotype to its phenotype.

Overview of the Central Dogma
The first step, transcription , involves the “copying” of information from a particular segment of DNA to a molecule of RNA. The segment of DNA that is copied typically encompasses one “gene”.

RNA uses the same language that DNA uses—nitrogenous bases—with one slight difference: RNA uses adenine (A), cytosine (C), and guanine (G), but instead of thymine (T), it uses a base called uracil (U). Uracil forms a complementary base pair with adenine. So, uracil appears in RNA wherever thymine would appear in DNA.

The RNA molecule produced is called messenger RNA (mRNA) —it leaves the cell’s nucleus (or nucleoid region) and carries the “message” to the cell’s ribosomes to be translated.

The second step, translation , is directed by the ribosomes in the cytoplasm. It involves decoding, or translating, the information stored in the nucleotide sequences of mRNA into corresponding amino acid sequences. As we’ve learned, amino acids are the monomers of proteins. The polypeptide chains produced during translation eventually form into fully-functioning proteins.

The Genetic Code
Although DNA and RNA are both nucleic acids and therefore can use base pairing to transfer genetic information, they are a chemically quite different. In fact, while there are only four different “letters” in the nucleic acid “alphabet,” there are actually 20 different kinds of amino acids making up proteins. This means that the process of translation literally involves translating a 4-letter language into a 20-letter language without the loss of any information.

The triplet code serves as a reference for how codons , or 3-letter base sequences of an RNA strand, are translated into single amino acids in ribosomes. Like all nucleic acid sequences, codons are written in the 5'→3' direction. Because codons involve three bases, the triplet code can theoretically code for 64 amino acids (4 3 ). This is much greater than the 20 codes for the naturally occurring amino acids, which means that the triplet code involves a fair number of redundancies .

The triplet code is summarized in a table in which the specific codon sequence is coupled with its corresponding amino acid. It is systematically arranged according to its first, second, and third mRNA bases beginning at the 5' end.

In order for an mRNA sequence to be translated into a polypeptide sequence, however, the mRNA sequence must be read in the correct reading frame . To do so, a sequence must be read in the correct direction, which is the 5'→3' direction or “downstream” direction.

Sequences must have distinct starting and ending points, which are indicated with a start codon (AUG, which also codes for methionine) and stop codons (UAA, UAG, and UGA). Sequences must also have clear rules about how to treat each base in the case of mRNA, codons do not overlap one another and there are no extraneous bases between the start and stop codons.

Transcription
The process of transcription resembles DNA replication in many ways and can be organized into three distinct stages.

The first step is initiation , in which RNA polymerase binds to a promoter , which is an initiating sequence in the DNA double helix located upstream of the gene. This causes the DNA strands to unwind enough to allow the polymerase to synthesize the RNA transcript . However, the DNA strands rapidly reform their base pairs and fold back into a double helix.

In prokaryotes, the polymerase immediately binds to DNA and initiates synthesis of the RNA transcript. In eukaryotes, a number of other proteins called transcription factors must first bind to DNA before the RNA polymerase can bind and begin RNA transcript synthesis. A core primer sequence is called the TATA box because it contains a specific sequence of adenine and thymine bases. It is the site for transcription factor binding.

The second step involves elongation , a process wherein the RNA polymerase moves downstream as it synthesizes the RNA transcript. The DNA double helix exposes only 10 to 20 nucleotides at a time for the polymerase. As in DNA replication, the polymerase adds new nucleotides to the 3' end of the growing RNA transcript.

Termination is the final step of transcription. In prokaryotes, termination occurs at particular terminator sequences , where the polymerase comes free of DNA and the RNA transcript is free to use. In eukaryotes, the RNA strand is cut free from the polymerase as what is called precursor mRNA or pre-mRNA . It must be processed in the nucleus first before it is able to exit.

RNA Modification
The pre-mRNA strand is reduced in length through a process of RNA splicing , in which noncoding segments within the strand called introns are spliced out. These introns are interspersed between the strands that will eventually be translated, which are called exons . The introns are recognized in part by an enzyme called a spliceosome , which coordinates with other special proteins to identify codes that surround the introns. This triggers their removal.

The resulting mRNA contains a 5' cap, which is a modified form of guanine after the transcription of the first 20 to 40 nucleotides. At 3' end, an enzyme adds a long stretch of adenine nucleotides. This forms what is called the poly(A) tail . This tail aids the mRNA in leaving the nucleus and in binding to the ribosome in the cytoplasm.

Translation
The process of translation follows a similar model as in transcription, involving the initation, elongation, and termination of a polypeptide chain. Three forms of RNA are involved in this process, each with a different function. A molecule of mRNA transfers the genetic information from DNA. Transfer RNA (tRNA) collects amino acids from the cytoplasm and transfers them to the ribosome, which contains ribosomal RNA (rRNA) .

Each tRNA molecule consists of a single-stranded oligonucleotide (about 80 nucleotides long) in the shape of an L. At the top part of the L is an anticodon , a complementary nucleotide triplet to the transcript codons that runs in a 3'→5' direction to form base pairs in an antiparallel fashion with the RNA transcript’s codons. The bottom part of the L is a covalently bound amino acid.

The redundancy in the genetic code is due to the fact that the pairing between the third base in the codon and the corresponding base in the tRNA anticodon is not strictly followed. This relaxation is known as wobble and explains why variability is allowed in the triplet’s third base in the genetic code. Amino acids in the cytoplasm are attached to the correct tRNA by the action of an enzyme called aminoacyl-tRNA synthetase of which there are 20, one for each amino acid. This enzyme binds to the same anticodons as the RNA transcript so that the redundancy is retained.

Translation
Ribosomes consist of large and small subunits made of proteins and rRNA. In each ribosome, there is an mRNA binding site and three tRNA binding sites in a row. The first tRNA binding site is called the A site , which is a holding site for the next amino acid in the chain. The middle binding site is called the P site , which binds the tRNA that is covalently connected to the growing polypeptide chain. The E site , or exit site, binds the amino-acid-free tRNA that is migrated from the P site and is released into the cytoplasm. The ribosome brings the mRNA and tRNA close together so that they can form a codon-anticodon base pair.

The chain initiation step begins when the small ribosomal subunit binds to both the RNA transcript and the start tRNA with the UAC anticodon and a methionine attached. The ribosomal unit reads the transcript downstream until it finds the AUG start codon. Finding this start codon establishes the proper reading frame. At that point, the bound tRNA forms a codon-anticodon base pair with the start codon. The large ribosomal unit and special proteins that aid in translation, called initiation factors , bind as well. The methionine-containing tRNA then rests in the P site with the A site awaiting another amino acid-bearing tRNA.

Translation
During chain elongation, an activated tRNA binds to the A site through codon recognition. The growing polypeptide chain that is attached to the P site tRNA transfers to the A site tRNA to form a new peptide bond. It attaches the A site tRNA’s amino acid to the end of the chain. Finally, the two tRNAs translocate by shifting down in the binding sites, such that the previous P site tRNA moves to the E site and the A site tRNA moves to the P site. In doing so, the amino-acid-free tRNA can exit the ribosome and the A site is ready for the next tRNA.

Chain elongation continues along the reading frame until a stop codon (UAA, UAG, or UGA) is reached at the A site. The stop codon binds to a protein called a release factor instead of a tRNA, and the release factor allows for the polypeptide chain to be hydrolyzed from the tRNA at the P site and float away. With no tRNAs at any of the sites, the two ribosomal subunits as well as the other components, disassociate.

Both prokaryotic and eukaryotic cells contain polyribosomes , which are strings of ribosomes that form around a transcript. Once the first ribosome begins processing the transcript, a ribosome can form around the free end and begin searching for the start codon. These strings of ribosomes allow for multiple polypeptides to be generated from a single transcript in a short period of time as the ribosomes migrate downstream.

The freed polypeptide is typically not ready for use, though it has undergone some folding. To become fully functional, it must undergo post-translational modifications. Although this allows proteins to then be used in prokaryotes, eukaryotes must mark the polypeptides with short signal peptides that direct the polypeptide to specific organelles.

Mutations
Changes in a cell’s genetic material are mutations . There are a number of ways that mutations can occur.

Some mutations occur from errors in replication or repair. When a chemical change occurs at a single base, it is called a point mutation . One type of point mutation is a base-pair substitution , in which one nucleotide is replaced by another. This may or may not be damaging, depending on where it ends up in a codon. For instance, if the mutation occurs at the third base in a codon, it may have no effect because of the redundancy at the wobble site and may just code for the wrong amino acid. These are referred to as missense mutations .

On the other hand, the mutation may create an unexpected stop codon, which is a called a nonsense mutation and often leads to a nonfunctional protein. Other kinds of point mutations include additions and deletions , which are called frameshift mutations because they alter the reading frame of the transcript. If three nucleotides were removed, this would involve the excision of an entire codon. The resulting protein would be missing a single amino acid. When one or more nucleotides are added or removed, however, the translation of the codon sequence is thrown off and will likely cause the wrong amino acid to be present throughout the rest of the polypeptide chain.

Mutations can also be caused when DNA interacts with harmful physical or chemical agents called mutagens . Physical agents, such as electromagnetic radiation (UV light or X-rays), can induce the breakdown of a nucleotide base. Chemical mutagens can also combine with or break down bases, or they can disrupt the normal flow of genetic material. They may have structural similarity to nucleotide bases and get incorporated into the DNA or RNA, thereby engaging in base pairing. Chemicals are tested for their mutagenic potential using a test known as the Ames test .


Funding to T.P. was provided by NHMRC Project APP1061551 and the NHMRC Senior Research Fellowship APP1135928. L.Y. was supported by the National Natural Science Foundation of China (NSFC) (grant numbers 31925011 and 91940306). The funding bodies had no role in study design, data collection or data analysis.

Ulrike Schumann and He-Na Zhang contributed equally to this work.

Affiliations

EMBL–Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia

Ulrike Schumann, Tennille Sibbritt, Anyu Pan, Attila Horvath, Simon Gross & Thomas Preiss

CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, New South Wales, Australia

Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales, 2010, Australia

School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010, Australia

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Contributions

T.P., U.S. and T.S. developed the study U.S., T.S., A.P. and S.G. performed experiments H.-N.Z. and A.H. performed bioinformatics analyses L.Y. and S.J.C. provided conceptual input U.S. and T.P. wrote the manuscript. The author(s) read and approved the final manuscript.

Corresponding author


Definition of Messenger RNA

Messenger RNA refers to an RNA sub-type that carries the specific codons corresponding to the DNA template and helps in the sequencing of amino acids to build various proteins by associating with the transfer RNA and ribosome.

Therefore, m-RNA serves as a DNA transcript that contains the information for the gene translation into protein. The formation of prokaryotic m-RNA is less complicated than the eukaryotic m-RNA. Messenger RNA exists as a short, single-stranded molecule that comprises a sugar-phosphate backbone.

Synthesis of m-RNA

In prokaryotes, messenger RNA synthesis occurs solely inside the cytoplasm as they lack a true nucleus. In eukaryotes, messenger RNA synthesis occurs inside the nucleus by using the nucleotide sequence of a template DNA strand.

Therefore, the template DNA transcribes the messenger RNA through a biological process known as “Transcription”. The RNA polymerase-II initiates the process of mRNA transcription by using a substrate (nucleotide triphosphate) from the template DNA strand.

Types of mRNA

Based on mRNA synthesis, the DNA transcribes into pre- mRNA and later transforms into a mature mRNA.

Pre- mRNA

It is an acronym for the term “Precursor mRNA”. Pre- mRNA refers to the primary transcript or immature mRNA, which belongs to the group of heterogeneous nuclear mRNA. Precursor mRNA comprises both coding exon sequences and non-coding intron sequences. During its processing, the unwanted sequences or introns splices out of the mRNA strand via two ways:

  • Splicing by the RNA’s catalytic activity.
  • Splicing by a multiprotein structure or spliceosome.

Mature mRNA

Further modifications in the pre- mRNA converts it into a mature mRNA transcript. Therefore, mature mRNA is derived after the maturation of pre- mRNA. Unlike pre- mRNA, it lacks introns.

For the translation of amino acids into proteins, 5’ capping and later tailing at the 3’ prime occurs in the mature mRNA. After processing, the mature mRNA exits nucleus and enters cytosol.

Then, the t-RNA plus ribosome decodes the information carried by mRNA to build proteins accordingly. Based on protein expression, the mRNA is categorized into the following types:

  1. Monocistronic mRNA: It is a kind of mRNA common in eukaryotes, which carries the exon sequences coding for a single protein.
  2. Bicistronic mRNA: It is a type of mRNA carrying exon sequences that encode two proteins.
  3. Polycistronic mRNA: It is a kind of mRNA common in bacteria and bacteriophages, which carries the exon sequences that code for the multiple proteins.

Structure of Messenger RNA

The structure of mature mRNA includes the following elements:

Coding sequences

The coding sequences of mature mRNA contains triplet codons. In eukaryotes, the triplet codons code for a specific amino acid and translate it into a single protein. Oppositely, the triplet codons in prokaryotes translate a gene into multiple proteins by the assistance of tRNA and ribosome.

The coding region begins with a “Start codon” (AUG) and ends with the “Termination codon” (UAA, UAG and UGA). Internal base pairs maintain the coding region. Coding region also functions as a regulating sequence, exonic splicing enhancer and inhibitors in the precursor mRNA.

Untranslated region

There are two untranslated regions in mature mRNA, one at 5’ prime and the other at 3’ prime. The 5’ untranslated region is present in between the 5’ cap and start codon. Conversely, 3’ untranslated region is present in between the stop codon and 3’ tail. The untranslated region is transcribed within the coding part. It performs the following functions like:

  • Stability of mRNA: Both 5’ and 3’ untranslated region regulates the mRNA stability, due to varying affinity for ribonucleases and ancillary proteins that can promote or inhibit RNA degradation.
  • Translational efficiency: 3’ or 5’ UTR may influence the transitional efficiency by controlling the ribosome’s ability to bind with the mRNA.
  • Localization of mRNA: This is regulated by 3’ UTR that contain sequences, which allow the transcript to be localized to the region for translation.
  • The untranslated region also contains some elements that regulate the mRNA:
  • SECIs element: It targets the proteins to bind.
  • Riboswitches: It directly binds the small molecules.

Poly (A) tail

A mature mRNA comprises a polyadenylated tail (up to 150-250 adenine bases) after the 3’ untranslated region. The Poly (A) tail performs the following functions in the mature mRNA:

  • 3′-tailing in eukaryotic mRNA helps in the transportation of mRNA residing within the nucleus into the cytoplasm.
  • The 3′ poly-A tailing protects the 3′-end of mature mRNA from degenerating.

A mature mRNA also comprises a 5’-cap before the 5’ untranslated region. The 7-methylguanosine cap associates with the 5’ end via 5’-5’ phosphate linkage, and it performs the following functions in mature mRNA:

  • The 5′-mRNA capping also protects the 5′-end of mature mRNA against degeneration.
  • 5′-capping in mRNA also directs the binding of the ribosomes during protein synthesis.

Functions of Messenger RNA

The messenger RNA performs a functional role in the process of gene expression by participating in the following tasks:

  1. An mRNA contains the source of genetic information from the template DNA that directs the amino acid formation.
  2. It also contains multiple regulatory regions that determine the rate and flow of translation.
  3. An mRNA contains the information on how to connect the amino acids into a peptide chain to form the proteins.

Conclusion

Therefore, the enzymatic activity of RNA polymerase on the DNA strand forms the mRNA (a sub-type of RNA). The messenger RNA transcription occurs from the 5′-3′ end and its further processing occurs before translation.

The transfer RNA in the cytosol possesses one specific anticodon arm that decodes the coding sequence of mRNA. After appropriate sequencing of amino acids, the transfer RNA loads the amino acids onto the ribosome, that results in protein synthesis.


Watch the video: Mnemonic for mRNA Stop Codons (May 2022).