Messenger RNA
Messenger ribonucleic acid is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.
mRNA is created during the process of transcription, where an enzyme converts the gene into primary transcript mRNA. This pre-mRNA usually still contains introns, regions that will not go on to code for the final amino acid sequence. These are removed in the process of RNA splicing, leaving only exons, regions that will encode the protein. This exon sequence constitutes mature mRNA. Mature mRNA is then read by the ribosome, and the ribosome creates the protein utilizing amino acids carried by transfer RNA. This process is known as translation. All of these processes form part of the central dogma of molecular biology, which describes the flow of genetic information in a biological system.
As in DNA, genetic information in mRNA is contained in the sequence of nucleotides, which are arranged into codons consisting of three ribonucleotides each. Each codon codes for a specific amino acid, except the stop codons, which terminate protein synthesis. The translation of codons into amino acids requires two other types of RNA: transfer RNA, which recognizes the codon and provides the corresponding amino acid, and ribosomal RNA, the central component of the ribosome's protein-manufacturing machinery.
The concept of mRNA was first conceived by Sydney Brenner and Francis Crick in 1960 during a conversation with François Jacob. In May 1961, messenger RNA was experimentally characterized in two back-to-back Nature papers: one by Brenner, Jacob, and Meselson, and one by Gros and colleagues. While analyzing the data in preparation for publication, Jacob and Jacques Monod coined the term "messenger RNA".
Synthesis
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 the process by which genetic information stored in DNA is copied into RNA by the enzyme RNA polymerase. During transcription, RNA polymerase binds to a promoter sequence on the DNA and synthesizes a complementary RNA strand from the DNA template.This process differs between prokaryotes and eukaryotes. In prokaryotes, transcription occurs in the cytoplasm. Because prokaryotes lack a membrane-bound nucleus, ribosomes can attach to the nascent mRNA strand and begin translation while transcription is still in progress.
In eukaryotes, transcription occurs within the cell nucleus. The initial product of transcription is not functional mRNA but is termed precursor mRNA or pre-mRNA. This pre-mRNA must undergo extensive processing to become mature mRNA. Once processed, the mature mRNA is exported from the nucleus to the cytoplasm for translation.
Uracil substitution for thymine
Whereas DNA contains thymine, RNA contains uracil. During the process of transcription, the enzyme RNA polymerase incorporates uracil opposite adenine bases located on the DNA template strand. Therefore, the resulting RNA transcript contains uracil in the positions where the coding DNA strand contains thymine.Structurally, uracil–adenine base pairs closely resemble thymine–adenine base pairs, which ensures that the genetic information carried by the sequence is faithfully preserved.
A frequently cited explanation for the presence of thymine in DNA involves the necessity of genome maintenance. Because cytosine can spontaneously deaminate to form uracil, DNA repair systems recognize uracil as a form of damage. The utilization of thymine as a standard base allows the cell to distinguish legitimate bases from errors, thereby maintaining uracil as a specific signal for repair.
Eukaryotic pre-mRNA processing
Processing of mRNA differs greatly among eukaryotes, bacteria, and archaea. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires several processing steps before its transport to the cytoplasm and its translation by the ribosome.Splicing
The extensive processing of eukaryotic pre-mRNA that leads to the mature mRNA is the RNA splicing, a mechanism by which introns or outrons are removed and exons are joined.5' cap addition
A 5' 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 molecule is edited, which changes the nucleotide composition of the transcript. A prominent example in humans involves the apolipoprotein B mRNA. In certain tissues, RNA editing of this transcript creates a premature stop codon, which results in the production of a shorter protein variant. Another well studied mechanism is A-to-I editing. This reaction is catalyzed by ADAR enzymes and typically occurs within double-stranded RNA regions. A-to-I editing may occur in both coding sequences and untranslated regions. Through these modifications, the process can affect protein recoding, RNA structure, and gene regulation.Polyadenylation
Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine are also common. The poly 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 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. Multiple mRNA export pathways have been identified in eukaryotes.In spatially complex cells, some mRNAs are transported to particular subcellular 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 β-actin mRNA. For export from the nucleus, actin mRNA associates with ZBP1 and later with 40S subunit. The complex is bound by a motor protein and is transported to the target location 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. mRNAs can also transfer between mammalian cells through structures called tunneling nanotubes.
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.In eukaryotic cells the process of translation starts with the information stored in the nucleotide sequence of DNA. This is first transformed into mRNA, then transfer RNA specifies which three-nucleotide codon from the genetic code corresponds to which amino acid.
Eukaryotic mRNA that has been processed and transported to the cytoplasm can then be translated by ribosomes. Translation may occur at ribosomes free in the cytoplasm, or targeted to the endoplasmic reticulum by the signal recognition particle. Therefore, unlike in prokaryotes, eukaryotic translation is not directly coupled to transcription. In some contexts, protein abundance can increase even when mRNA abundance decreases, because translation efficiency and protein turnover are regulated independently of transcript levels; this has been reported for mRNA and protein levels of EEF1A1 in breast cancer.