Messenger RNA | Wikipedia audio article

Messenger RNA | Wikipedia audio article


Messenger RNA (mRNA) is a large family of
RNA molecules that convey genetic information from DNA to the ribosome, where they specify
the amino acid sequence of the protein products of gene expression. The RNA polymerase enzyme transcribes genes
into primary transcript mRNA (known as pre-mRNA) leading to processed, mature mRNA. This mature mRNA is then translated into a
polymer of amino acids: a protein, as summarized in the central dogma of molecular biology. As in DNA, mRNA genetic information is in
the sequence of nucleotides, which are arranged into codons consisting of three base pairs
each. Each codon encodes for a specific amino acid,
except the stop codons, which terminate protein synthesis. This process of translation of codons into
amino acids requires two other types of RNA: Transfer RNA (tRNA), that mediates recognition
of the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), that
is the central component of the ribosome’s protein-manufacturing machinery. The existence of mRNA was first suggested
by Jacques Monod and François Jacob, and subsequently discovered by Jacob, Sydney Brenner
and Matthew Meselson at the California Institute of Technology in 1961. It should not be confused with mitochondrial
DNA.==Synthesis, processing and function==
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 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 (non-coding
regions) are removed and exons (coding regions) are joined together.====5′ cap addition====A 5′ cap (also termed an RNA cap, an RNA 7-methylguanosine
cap, or an RNA m7G 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 apolipopropein
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 β-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. It is even possible in some contexts that
reduced mRNA levels are accompanied by increased protein levels, as has been observed for mRNA/protein
levels of EEF1A1 in breast cancer.==Structure=====Coding regions===Coding regions are composed of codons, which
are decoded and translated (in eukaryotes usually into one and in prokaryotes usually
into several) into proteins by the ribosome. Coding regions begin with the start codon
and end with a stop codon. In general, the start codon is an AUG triplet
and the stop codon is UAA, UAG, or UGA. The coding regions tend to be stabilised by
internal base pairs, this impedes degradation. In addition to being protein-coding, portions
of coding regions may serve as regulatory sequences in the pre-mRNA as exonic splicing
enhancers or exonic splicing silencers.===Untranslated regions===Untranslated regions (UTRs) are sections of
the mRNA before the start codon and after the stop codon that are not translated, termed
the five prime untranslated region (5′ UTR) and three prime untranslated region (3′ UTR),
respectively. These regions are transcribed with the coding
region and thus are exonic as they are present in the mature mRNA. Several roles in gene expression have been
attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational
efficiency. The ability of a UTR to perform these functions
depends on the sequence of the UTR and can differ between mRNAs. Genetic variants in 3′ UTR have also been
implicated in disease susceptibility because of the change in RNA structure and protein
translation.The stability of mRNAs may be controlled by the 5′ UTR and/or 3′ UTR due
to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins
that can promote or inhibit RNA degradation. (See also, C-rich stability element.) Translational efficiency, including sometimes
the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3′ or 5′
UTR may affect translation by influencing the ribosome’s ability to bind to the mRNA. MicroRNAs bound to the 3′ UTR also may affect
translational efficiency or mRNA stability. Cytoplasmic localization of mRNA is thought
to be a function of the 3′ UTR. Proteins that are needed in a particular region
of the cell can also be translated there; in such a case, the 3′ UTR may contain sequences
that allow the transcript to be localized to this region for translation. Some of the elements contained in untranslated
regions form a characteristic secondary structure when transcribed into RNA. These structural mRNA elements are involved
in regulating the mRNA. Some, such as the SECIS element, are targets
for proteins to bind. One class of mRNA element, the riboswitches,
directly bind small molecules, changing their fold to modify levels of transcription or
translation. In these cases, the mRNA regulates itself.===Poly(A) tail===The 3′ poly(A) tail is a long sequence of
adenine nucleotides (often several hundred) added to the 3′ end of the pre-mRNA. This tail promotes export from the nucleus
and translation, and protects the mRNA from degradation.===Monocistronic versus polycistronic mRNA
===An mRNA molecule is said to be monocistronic
when it contains the genetic information to translate only a single protein chain (polypeptide). This is the case for most of the eukaryotic
mRNAs. On the other hand, polycistronic mRNA carries
several open reading frames (ORFs), each of which is translated into a polypeptide. These polypeptides usually have a related
function (they often are the subunits composing a final complex protein) and their coding
sequence is grouped and regulated together in a regulatory region, containing a promoter
and an operator. Most of the mRNA found in bacteria and archaea
is polycistronic, as is the human mitochondrial genome. Dicistronic or bicistronic mRNA encodes only
two proteins.===mRNA circularization===
In eukaryotes mRNA molecules form circular structures due to an interaction between the
eIF4E and poly(A)-binding protein, which both bind to eIF4G, forming an mRNA-protein-mRNA
bridge. Circularization is thought to promote cycling
of ribosomes on the mRNA leading to time-efficient translation, and may also function to ensure
only intact mRNA are translated (partially degraded mRNA characteristically have no m7G
cap, or no poly-A tail).Other mechanisms for circularization exist, particularly in virus
mRNA. Poliovirus mRNA uses a cloverleaf section
towards its 5′ end to bind PCBP2, which binds poly(A)-binding protein, forming the familiar
mRNA-protein-mRNA circle. Barley yellow dwarf virus has binding between
mRNA segments on its 5′ end and 3′ end (called kissing stem loops), circularizing the mRNA
without any proteins involved. RNA virus genomes (the + strands of which
are translated as mRNA) are also commonly circularized.Template:Cite journal needed
During genome replication the circularization acts to enhance genome replication speeds,
cycling viral RNA-dependent RNA polymerase much the same as the ribosome is hypothesized
to cycle.==Degradation==
Different mRNAs within the same cell have distinct lifetimes (stabilities). In bacterial cells, individual mRNAs can survive
from seconds to more than an hour. However, the lifetime averages between 1 and
3 minutes, making bacterial mRNA much less stable than eukaryotic mRNA. In mammalian cells, mRNA lifetimes range from
several minutes to days. The greater the stability of an mRNA the more
protein may be produced from that mRNA. The limited lifetime of mRNA enables a cell
to alter protein synthesis rapidly in response to its changing needs. There are many mechanisms that lead to the
destruction of an mRNA, some of which are described below.===Prokaryotic mRNA degradation===
In general, in prokaryotes the lifetime of mRNA is much shorter than in eukaryotes. Prokaryotes degrade messages by using a combination
of ribonucleases, including endonucleases, 3′ exonucleases, and 5′ exonucleases. In some instances, small RNA molecules (sRNA)
tens to hundreds of nucleotides long can stimulate the degradation of specific mRNAs by base-pairing
with complementary sequences and facilitating ribonuclease cleavage by RNase III. It was recently shown that bacteria also have
a sort of 5′ cap consisting of a triphosphate on the 5′ end. Removal of two of the phosphates leaves a
5′ monophosphate, causing the message to be destroyed by the exonuclease RNase J, which
degrades 5′ to 3′.===Eukaryotic mRNA turnover===
Inside eukaryotic cells, there is a balance between the processes of translation and mRNA
decay. Messages that are being actively translated
are bound by ribosomes, the eukaryotic initiation factors eIF-4E and eIF-4G, and poly(A)-binding
protein. eIF-4E and eIF-4G block the decapping enzyme
(DCP2), and poly(A)-binding protein blocks the exosome complex, protecting the ends of
the message. The balance between translation and decay
is reflected in the size and abundance of cytoplasmic structures known as P-bodies The
poly(A) tail of the mRNA is shortened by specialized exonucleases that are targeted to specific
messenger RNAs by a combination of cis-regulatory sequences on the RNA and trans-acting RNA-binding
proteins. Poly(A) tail removal is thought to disrupt
the circular structure of the message and destabilize the cap binding complex. The message is then subject to degradation
by either the exosome complex or the decapping complex. In this way, translationally inactive messages
can be destroyed quickly, while active messages remain intact. The mechanism by which translation stops and
the message is handed-off to decay complexes is not understood in detail.===AU-rich element decay===
The presence of AU-rich elements in some mammalian mRNAs tends to destabilize those transcripts
through the action of cellular proteins that bind these sequences and stimulate poly(A)
tail removal. Loss of the poly(A) tail is thought to promote
mRNA degradation by facilitating attack by both the exosome complex and the decapping
complex. Rapid mRNA degradation via AU-rich elements
is a critical mechanism for preventing the overproduction of potent cytokines such as
tumor necrosis factor (TNF) and granulocyte-macrophage colony stimulating factor (GM-CSF). AU-rich elements also regulate the biosynthesis
of proto-oncogenic transcription factors like c-Jun and c-Fos.===
Nonsense mediated decay===Eukaryotic messages are subject to surveillance
by nonsense mediated decay (NMD), which checks for the presence of premature stop codons
(nonsense codons) in the message. These can arise via incomplete splicing, V(D)J
recombination in the adaptive immune system, mutations in DNA, transcription errors, leaky
scanning by the ribosome causing a frame shift, and other causes. Detection of a premature stop codon triggers
mRNA degradation by 5′ decapping, 3′ poly(A) tail removal, or endonucleolytic cleavage.===Small interfering RNA (siRNA)===In metazoans, small interfering RNAs (siRNAs)
processed by Dicer are incorporated into a complex known as the RNA-induced silencing
complex or RISC. This complex contains an endonuclease that
cleaves perfectly complementary messages to which the siRNA binds. The resulting mRNA fragments are then destroyed
by exonucleases. siRNA is commonly used in laboratories to
block the function of genes in cell culture. It is thought to be part of the innate immune
system as a defense against double-stranded RNA viruses.===MicroRNA (miRNA)===MicroRNAs (miRNAs) are small RNAs that typically
are partially complementary to sequences in metazoan messenger RNAs. Binding of a miRNA to a message can repress
translation of that message and accelerate poly(A) tail removal, thereby hastening mRNA
degradation. The mechanism of action of miRNAs is the subject
of active research.===Other decay mechanisms===
There are other ways by which messages can be degraded, including non-stop decay and
silencing by Piwi-interacting RNA (piRNA), among others.==mRNA-based therapeutics==
Full length mRNA molecules have been proposed as therapeutics since the beginning of the
biotech era but there was little traction until the 2010s, when Moderna Therapeutics
was founded and managed to raise almost a billion dollars in venture funding in its
first three years.Theoretically, the administered mRNA sequence can cause a cell to make a protein,
which in turn could directly treat a disease or could function as a vaccine; more indirectly
the protein could drive an endogenous stem cell to differentiate in a desired way.The
primary challenges of RNA therapy center on delivering the RNA to directed cells, more
even than determining what sequence to deliver. Naked RNA sequences will naturally degrade
after preparation; they may trigger the body’s immune system to attack them as an invader;
and they are impermeable to the cell membrane. Once within the cell, they must then leave
the cell’s transport mechanism to take action within the cytoplasm, which houses the ribosomes
that direct manufacture of proteins.==See also==
GeneCalling, an mRNA profiling technology Transcriptome, the sum of all RNA in a cell

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