93-408: Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates ; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes , polyadenylation is part of the process that produces mature mRNA for translation . In many bacteria , the poly(A) tail promotes degradation of
186-503: A "termination sequence" (⁵'TTTATT' on the DNA template and ⁵'AAUAAA' on the primary transcript), the end of transcription is signaled. The polyadenylation machinery is also physically linked to the spliceosome , a complex that removes introns from RNAs. The poly(A) tail acts as the binding site for poly(A)-binding protein . Poly(A)-binding protein promotes export from the nucleus and translation, and inhibits degradation. This protein binds to
279-459: 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 the appropriate cells. Challenges include the fact that naked RNA sequences naturally degrade after preparation; they may trigger
372-473: 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
465-625: 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. MicroRNAs (miRNAs) are small RNAs that typically are partially complementary to sequences in metazoan messenger RNAs. Binding of
558-565: 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. 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
651-433: 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. There are other ways by which messages can be degraded, including non-stop decay and silencing by Piwi-interacting RNA (piRNA), among others. The administration of a nucleoside-modified messenger RNA sequence can cause
744-420: A poly(A) tail is added to an RNA at the end of transcription. On mRNAs, the poly(A) tail protects the mRNA molecule from enzymatic degradation in the cytoplasm and aids in transcription termination, export of the mRNA from the nucleus, and translation. Almost all eukaryotic mRNAs are polyadenylated, with the exception of animal replication-dependent histone mRNAs. These are the only mRNAs in eukaryotes that lack
837-409: A poly(A) tail, ending instead in a stem-loop structure followed by a purine-rich sequence, termed histone downstream element, that directs where the RNA is cut so that the 3′ end of the histone mRNA is formed. Many eukaryotic non-coding RNAs are always polyadenylated at the end of transcription. There are small RNAs where the poly(A) tail is seen only in intermediary forms and not in the mature RNA as
930-701: A series of experiments whose results pointed in roughly the same direction. Brenner and the others agreed to Watson's request to delay publication of their research findings. As a result, the Brenner and Watson articles were published simultaneously in the same issue of Nature in May 1961, while that same month, Jacob and Monod published their theoretical framework for mRNA in the Journal of Molecular Biology . Cleavage stimulatory factor Cleavage stimulatory factor or cleavage stimulation factor ( CstF or CStF )
1023-490: A single gene ( alternative polyadenylation ), similar to alternative splicing . The poly(A) tail is important for the nuclear export, translation and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. However, in a few cell types, mRNAs with short poly(A) tails are stored for later activation by re-polyadenylation in the cytosol. In contrast, when polyadenylation occurs in bacteria, it promotes RNA degradation. This
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#17327752756911116-496: A tail that is around 4 nucleotides long to the 3′ end. The RNA is then degraded by the exosome . Poly(A) tails have also been found on human rRNA fragments, both the form of homopolymeric (A only) and heterpolymeric (mostly A) tails. In many bacteria, both mRNAs and non-coding RNAs can be polyadenylated. This poly(A) tail promotes degradation by the degradosome , which contains two RNA-degrading enzymes: polynucleotide phosphorylase and RNase E . Polynucleotide phosphorylase binds to
1209-443: A transcript contains many polyadenylation signals (PAS). When more proximal (closer towards 5’ end) PAS sites are utilized, this shortens the length of the 3’ untranslated region (3' UTR) of a transcript. Studies in both humans and flies have shown tissue specific APA. With neuronal tissues preferring distal PAS usage, leading to longer 3’ UTRs and testis tissues preferring proximal PAS leading to shorter 3’ UTRs. Studies have shown there
1302-420: Is initiation factor -4G, which in turn recruits the 40S ribosomal subunit. However, a poly(A) tail is not required for the translation of all mRNAs. Further, poly(A) tailing (oligo-adenylation) can determine the fate of RNA molecules that are usually not poly(A)-tailed (such as (small) non-coding (sn)RNAs etc.) and thereby induce their RNA decay. In eukaryotic somatic cells , the poly(A) tails of most mRNAs in
1395-401: Is a heterotrimeric protein , made up of the proteins CSTF1 (55 kDa ), CSTF2 (64kDa) and CSTF3 (77kDa), totalling about 200 kDa. It is involved in the cleavage of the 3' signaling region from a newly synthesized pre- messenger RNA (mRNA) molecule. CstF is recruited by cleavage and polyadenylation specificity factor (CPSF) and assembles into a protein complex on the 3' end to promote
1488-408: Is a correlation between a gene's conservation level and its tendency to do alternative polyadenylation, with highly conserved genes exhibiting more APA. Similarly, highly expressed genes follow this same pattern. Ribo-sequencing data (sequencing of only mRNAs inside ribosomes) has shown that mRNA isoforms with shorter 3’ UTRs are more likely to be translated. Since alternative polyadenylation changes
1581-429: 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 ( RNA polymerase ) converts the gene into primary transcript mRNA (also known as pre-mRNA ). This pre-mRNA usually still contains introns , regions that will not go on to code for
1674-403: Is also sometimes the case for eukaryotic non-coding RNAs . mRNA molecules in both prokaryotes and eukaryotes have polyadenylated 3′-ends, with the prokaryotic poly(A) tails generally shorter and fewer mRNA molecules polyadenylated. RNAs are a type of large biological molecules, whose individual building blocks are called nucleotides. The name poly(A) tail (for polyadenylic acid tail) reflects
1767-450: Is also where the poly(A) tail is found on polyadenylated RNAs. Messenger RNA (mRNA) is RNA that has a coding region that acts as a template for protein synthesis ( translation ). The rest of the mRNA, the untranslated regions , tune how active the mRNA is. There are also many RNAs that are not translated, called non-coding RNAs. Like the untranslated regions, many of these non-coding RNAs have regulatory roles. In nuclear polyadenylation,
1860-417: 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
1953-599: 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. mRNAs can also transfer between mammalian cells through structures called tunneling nanotubes . Because prokaryotic mRNA does not need to be processed or transported, translation by
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#17327752756912046-418: Is found in bacteria, mitochondria, plastids and as a constituent of the archaeal exosome (in those archaea that have an exosome ). It can synthesise a 3′ extension where the vast majority of the bases are adenines. Like in bacteria, polyadenylation by polynucleotide phosphorylase promotes degradation of the RNA in plastids and likely also archaea. Although polyadenylation is seen in almost all organisms, it
2139-520: Is homologous to that of other polymerases . It is presumed that the horizontal transfer of bacterial CCA-adding enzyme to eukaryotes allowed the archaeal-like CCA-adding enzyme to switch function to a poly(A) polymerase. Some lineages, like archaea and cyanobacteria , never evolved a polyadenylate polymerase. Polyadenylate tails are observed in several RNA viruses , including Influenza A , Coronavirus , Alfalfa mosaic virus , and Duck Hepatitis A . Some viruses, such as HIV-1 and Poliovirus , inhibit
2232-491: Is not universal. However, the wide distribution of this modification and the fact that it is present in organisms from all three domains of life implies that the last universal common ancestor of all living organisms, it is presumed, had some form of polyadenylation system. A few organisms do not polyadenylate mRNA, which implies that they have lost their polyadenylation machineries during evolution. Although no examples of eukaryotes that lack polyadenylation are known, mRNAs from
2325-586: Is termed mature mRNA . mRNA uses uracil (U) instead of thymine (T) in DNA. uracil (U) is the complementary base to adenine (A) during transcription instead of thymine (T). Thus, when using a template strand of DNA to build RNA, thymine is replaced with uracil. This substitution allows the mRNA to carry the appropriate genetic information from DNA to the ribosome for translation. Regarding the natural history, uracil came first then thymine; evidence suggests that RNA came before DNA in evolution. The RNA World hypothesis proposes that life began with RNA molecules, before
2418-486: 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 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
2511-431: 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
2604-472: The 5′ cap and remove nucleotides from the poly(A) tail. The level of access to the 5′ cap and poly(A) tail is important in controlling how soon the mRNA is degraded. PARN deadenylates less if the RNA is bound by the initiation factors 4E (at the 5′ cap) and 4G (at the poly(A) tail), which is why translation reduces deadenylation. The rate of deadenylation may also be regulated by RNA-binding proteins. Additionally, RNA triple helix structures and RNA motifs such as
2697-598: The California Institute of Technology for assistance. During the summer of 1960, Brenner, Jacob, and Meselson conducted an experiment in Meselson's laboratory at Caltech which was the first to prove the existence of mRNA. That fall, Jacob and Monod coined the name "messenger RNA" and developed the first theoretical framework to explain its function. In February 1961, James Watson revealed that his Harvard -based research group had been right behind them with
2790-542: 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
2883-445: 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 . Coding regions are composed of codons , which are decoded and translated into proteins by
Polyadenylation - Misplaced Pages Continue
2976-487: 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
3069-418: The germline , during early embryogenesis and in post- synaptic sites of nerve cells . This lengthens the poly(A) tail of an mRNA with a shortened poly(A) tail, so that the mRNA will be translated . These shortened poly(A) tails are often less than 20 nucleotides, and are lengthened to around 80–150 nucleotides. In the early mouse embryo, cytoplasmic polyadenylation of maternal RNAs from the egg cell allows
3162-676: The mitochondria contain both stabilising and destabilising poly(A) tails. Destabilising polyadenylation targets both mRNA and noncoding RNAs. The poly(A) tails are 43 nucleotides long on average. The stabilising ones start at the stop codon, and without them the stop codon (UAA) is not complete as the genome only encodes the U or UA part. Plant mitochondria have only destabilising polyadenylation. Mitochondrial polyadenylation has never been observed in either budding or fission yeast. While many bacteria and mitochondria have polyadenylate polymerases, they also have another type of polyadenylation, performed by polynucleotide phosphorylase itself. This enzyme
3255-404: 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 subcellular destinations. In mature neurons , certain mRNA are transported from the soma to dendrites . One site of mRNA translation
3348-418: The pre-mRNA as exonic splicing enhancers or exonic splicing silencers . 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
3441-406: 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
3534-434: 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
3627-418: The 1990s, mRNA vaccines for personalized cancer have been developed, relying on non-nucleoside modified mRNA. mRNA based therapies continue to be investigated as a method of treatment or therapy for both cancer as well as auto-immune, metabolic, and respiratory inflammatory diseases. Gene editing therapies such as CRISPR may also benefit from using mRNA to induce cells to make the desired Cas protein. Since
3720-572: The 2010s, RNA vaccines and other RNA therapeutics have been considered to be "a new class of drugs". The first mRNA-based vaccines received restricted authorization and were rolled out across the world during the COVID-19 pandemic by Pfizer–BioNTech COVID-19 vaccine and Moderna , for example. The 2023 Nobel Prize in Physiology or Medicine was awarded to Katalin Karikó and Drew Weissman for
3813-558: The 3′ end of RNAs and the 3′ extension provided by the poly(A) tail allows it to bind to the RNAs whose secondary structure would otherwise block the 3′ end. Successive rounds of polyadenylation and degradation of the 3′ end by polynucleotide phosphorylase allows the degradosome to overcome these secondary structures. The poly(A) tail can also recruit RNases that cut the RNA in two. These bacterial poly(A) tails are about 30 nucleotides long. In as different groups as animals and trypanosomes ,
Polyadenylation - Misplaced Pages Continue
3906-419: The 3′ untranslated region. The choice of poly(A) site can be influenced by extracellular stimuli and depends on the expression of the proteins that take part in polyadenylation. For example, the expression of CstF-64 , a subunit of cleavage stimulatory factor (CstF), increases in macrophages in response to lipopolysaccharides (a group of bacterial compounds that trigger an immune response). This results in
3999-511: The 3′-most nucleotides with a phosphate, breaking off a diphosphate nucleotide. This reaction is reversible, and so the enzyme can also extend RNA with more nucleotides. The heteropolymeric tail added by polynucleotide phosphorylase is very rich in adenine. The choice of adenine is most likely the result of higher ADP concentrations than other nucleotides as a result of using ATP as an energy currency, making it more likely to be incorporated in this tail in early lifeforms. It has been suggested that
4092-408: 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
4185-482: The RNA cleavage complex – varies between groups of eukaryotes. Most human polyadenylation sites contain the AAUAAA sequence, but this sequence is less common in plants and fungi. The RNA is typically cleaved before transcription termination, as CstF also binds to RNA polymerase II. Through a poorly understood mechanism (as of 2002), it signals for RNA polymerase II to slip off of the transcript. Cleavage also involves
4278-412: The RNA, but variants of it that bind more weakly to CPSF exist. Two other proteins add specificity to the binding to an RNA: CstF and CFI. CstF binds to a GU-rich region further downstream of CPSF's site. CFI recognises a third site on the RNA (a set of UGUAA sequences in mammals) and can recruit CPSF even if the AAUAAA sequence is missing. The polyadenylation signal – the sequence motif recognised by
4371-489: The RNA-binding proteins CPSF and CPEB , and can involve other RNA-binding proteins like Pumilio . Depending on the cell type, the polymerase can be the same type of polyadenylate polymerase (PAP) that is used in the nuclear process, or the cytoplasmic polymerase GLD-2 . Many protein-coding genes have more than one polyadenylation site, so a gene can code for several mRNAs that differ in their 3′ end . The 3’ region of
4464-401: The bacterium Mycoplasma gallisepticum and the salt-tolerant archaean Haloferax volcanii lack this modification. The most ancient polyadenylating enzyme is polynucleotide phosphorylase . This enzyme is part of both the bacterial degradosome and the archaeal exosome , two closely related complexes that recycle RNA into nucleotides. This enzyme degrades RNA by attacking the bond between
4557-430: 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 necessary ribosomes . Overcoming these challenges, mRNA as a therapeutic was first put forward in 1989 "after the development of a broadly applicable in vitro transfection technique." In
4650-455: The cell to survive and grow even though transcription does not start until the middle of the 2-cell stage (4-cell stage in human). In the brain, cytoplasmic polyadenylation is active during learning and could play a role in long-term potentiation , which is the strengthening of the signal transmission from a nerve cell to another in response to nerve impulses and is important for learning and memory formation. Cytoplasmic polyadenylation requires
4743-457: The cell's poly-A binding protein ( PABPC1 ) in order to emphasize their own genes' expression over the host cell's. Poly(A)polymerase was first identified in 1960 as an enzymatic activity in extracts made from cell nuclei that could polymerise ATP, but not ADP, into polyadenine. Although identified in many types of cells, this activity had no known function until 1971, when poly(A) sequences were found in mRNAs. The only function of these sequences
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#17327752756914836-461: The codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), the central component of the ribosome's protein-manufacturing machinery. The concept of mRNA was developed by Sydney Brenner and Francis Crick in 1960 during a conversation with François Jacob . In 1961, mRNA was identified and described independently by one team consisting of Brenner, Jacob, and Matthew Meselson , and another team led by James Watson . While analyzing
4929-465: The cytoplasm and its translation by the ribosome. 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. A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m G cap) is a modified guanine nucleotide that has been added to
5022-609: The cytoplasm gradually get shorter, and mRNAs with shorter poly(A) tail are translated less and degraded sooner. However, it can take many hours before an mRNA is degraded. This deadenylation and degradation process can be accelerated by microRNAs complementary to the 3′ untranslated region of an mRNA. In immature egg cells , mRNAs with shortened poly(A) tails are not degraded, but are instead stored and translationally inactive. These short tailed mRNAs are activated by cytoplasmic polyadenylation after fertilisation, during egg activation . In animals, poly(A) ribonuclease ( PARN ) can bind to
5115-462: The data in preparation for publication, Jacob and Jacques Monod coined the name "messenger RNA". 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
5208-521: The destruction of an mRNA, some of which are described below. 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
5301-400: The development of effective mRNA vaccines against COVID-19. Several molecular biology studies during the 1950s indicated that RNA played some kind of role in protein synthesis, but that role was not clearly understood. For instance, in one of the earliest reports, Jacques Monod and his team showed that RNA synthesis was necessary for protein synthesis, specifically during the production of
5394-469: 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,
5487-476: The emergence of DNA genomes and coded proteins. In DNA, the evolutionary substitution of thymine for uracil may have increased DNA stability and improved the efficiency of DNA replication. 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
5580-626: The ends are removed during processing, the notable ones being microRNAs . But, for many long noncoding RNAs – a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist , which mediates X chromosome inactivation – a poly(A) tail is part of the mature RNA. CPSF : cleavage/polyadenylation specificity factor CstF : cleavage stimulation factor PAP : polyadenylate polymerase PABII : polyadenylate binding protein 2 CFI : cleavage factor I CFII : cleavage factor II The processive polyadenylation complex in
5673-404: The enzyme β-galactosidase in the bacterium E. coli . Arthur Pardee also found similar RNA accumulation in 1954 . In 1953, Alfred Hershey , June Dixon, and Martha Chase described a certain cytosine-containing DNA (indicating it was RNA) that disappeared quickly after its synthesis in E. coli . In hindsight, this may have been one of the first observations of the existence of mRNA but it
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#17327752756915766-403: 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 (tRNA). This process is known as translation . All of these processes form part of
5859-405: The involvement of adenine-rich tails in RNA degradation prompted the later evolution of polyadenylate polymerases (the enzymes that produce poly(A) tails with no other nucleotides in them). Polyadenylate polymerases are not as ancient. They have separately evolved in both bacteria and eukaryotes from CCA-adding enzyme , which is the enzyme that completes the 3′ ends of tRNAs . Its catalytic domain
5952-434: The length of the 3' UTR , it can also change which binding sites are available for microRNAs in the 3′ UTR. MicroRNAs tend to repress translation and promote degradation of the mRNAs they bind to, although there are examples of microRNAs that stabilise transcripts. Alternative polyadenylation can also shorten the coding region, thus making the mRNA code for a different protein, but this is much less common than just shortening
6045-419: 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
6138-448: 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
6231-418: The mRNA found in bacteria and archaea is polycistronic, as is the human mitochondrial genome. Dicistronic or bicistronic mRNA encodes only two proteins . 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
6324-561: 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
6417-408: The mRNA regulates itself. 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. An mRNA molecule is said to be monocistronic when it contains the genetic information to translate only a single protein chain (polypeptide). This
6510-499: The mRNA without any proteins involved. RNA virus genomes (the + strands of which are translated as mRNA) are also commonly circularized. 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. 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,
6603-482: The mRNA. It, therefore, forms part of the larger process of gene expression . The process of polyadenylation begins as the transcription of a gene terminates . The 3′-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins ; these proteins then synthesize the poly(A) tail at the RNA's 3′ end. In some genes these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from
6696-528: 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
6789-435: The message is handed-off to decay complexes is not understood in detail. The majority of mRNA decay was believed to be cytoplasmic; however, recently, a novel mRNA decay pathway was described, which starts in the nucleus. 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
6882-460: The new mRNA strand to become double stranded by producing a complementary strand known as the tRNA strand, which when combined are unable to form structures from base-pairing. Moreover, the template for mRNA is the complementary strand of tRNA, which is identical in sequence to the anticodon sequence that the DNA binds to. The short-lived, unprocessed or partially processed product is termed precursor mRNA , or pre-mRNA ; once completely processed, it
6975-410: The new, short poly(A) tail and increases the affinity of polyadenylate polymerase for the RNA. When the poly(A) tail is approximately 250 nucleotides long the enzyme can no longer bind to CPSF and polyadenylation stops, thus determining the length of the poly(A) tail. CPSF is in contact with RNA polymerase II, allowing it to signal the polymerase to terminate transcription. When RNA polymerase II reaches
7068-435: The nucleus of eukaryotes works on products of RNA polymerase II , such as precursor mRNA . Here, a multi-protein complex (see components on the right) cleaves the 3′-most part of a newly produced RNA and polyadenylates the end produced by this cleavage. The cleavage is catalysed by the enzyme CPSF and occurs 10–30 nucleotides downstream of its binding site. This site often has the polyadenylation signal sequence AAUAAA on
7161-442: 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. In some instances, an mRNA will be edited , changing the nucleotide composition of that mRNA. An example in humans
7254-474: The poly(A) tail 3’ end binding pocket retard deadenylation process and inhibit poly(A) tail removal. Once the poly(A) tail is removed, the decapping complex removes the 5′ cap, leading to a degradation of the RNA. Several other proteins are involved in deadenylation in budding yeast and human cells, most notably the CCR4-Not complex. There is polyadenylation in the cytosol of some animal cell types, namely in
7347-582: 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 . Eukaryotic messages are subject to surveillance by nonsense-mediated decay (NMD), which checks for
7440-416: The poly(A) tail prior to mRNA export from the nucleus and in yeast also recruits poly(A) nuclease, an enzyme that shortens the poly(A) tail and allows the export of the mRNA. Poly(A)-binding protein is exported to the cytoplasm with the RNA. mRNAs that are not exported are degraded by the exosome . Poly(A)-binding protein also can bind to, and thus recruit, several proteins that affect translation, one of these
7533-458: The polyadenylation signal. In addition, numerous other components involved in transcription, splicing or other mechanisms regulating RNA biology can affect APA. For many non-coding RNAs , including tRNA , rRNA , snRNA , and snoRNA , polyadenylation is a way of marking the RNA for degradation, at least in yeast . This polyadenylation is done in the nucleus by the TRAMP complex , which maintains
7626-516: 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 . In metazoans , small interfering RNAs (siRNAs) processed by Dicer are incorporated into
7719-476: The protein CFII, though it is unknown how. The cleavage site associated with a polyadenylation signal can vary up to some 50 nucleotides. When the RNA is cleaved, polyadenylation starts, catalysed by polyadenylate polymerase. Polyadenylate polymerase builds the poly(A) tail by adding adenosine monophosphate units from adenosine triphosphate to the RNA, cleaving off pyrophosphate . Another protein, PAB2, binds to
7812-474: 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,
7905-464: The proteins surrounding it are together called a messenger RNP . Transcription is when RNA is copied from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process differs slightly in eukaryotes and prokaryotes. One notable difference is that prokaryotic RNA polymerase associates with DNA-processing enzymes during transcription so that processing can proceed during transcription. Therefore, this causes
7998-438: 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
8091-467: The ribosome; in eukaryotes usually into one and in prokaryotes usually into several. 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 UAG ("amber"), UAA ("ochre"), or UGA ("opal"). 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
8184-429: The selection of weak poly(A) sites and thus shorter transcripts. This removes regulatory elements in the 3′ untranslated regions of mRNAs for defense-related products like lysozyme and TNF-α . These mRNAs then have longer half-lives and produce more of these proteins. RNA-binding proteins other than those in the polyadenylation machinery can also affect whether a polyadenylation site is used, as can DNA methylation near
8277-418: The synthesis of a functional polyadenine tail , which results in a mature mRNA molecule ready to be exported from the cell nucleus to the cytosol for translation . The amount of CstF in a cell is dependent on the phase of the cell cycle , increasing significantly during the transition from G0 phase to S phase in mouse fibroblast and human splenic B cells . This protein -related article
8370-406: The way RNA nucleotides are abbreviated, with a letter for the base the nucleotide contains (A for adenine , C for cytosine , G for guanine and U for uracil ). RNAs are produced ( transcribed ) from a DNA template. By convention, RNA sequences are written in a 5′ to 3′ direction. The 5′ end is the part of the RNA molecule that is transcribed first, and the 3′ end is transcribed last. The 3′ end
8463-535: Was not recognized at the time as such. The idea of mRNA was first conceived by Sydney Brenner and Francis Crick on 15 April 1960 at King's College, Cambridge , while François Jacob was telling them about a recent experiment conducted by Arthur Pardee , himself, and Monod (the so-called PaJaMo experiment, which did not prove mRNA existed but suggested the possibility of its existence). With Crick's encouragement, Brenner and Jacob immediately set out to test this new hypothesis, and they contacted Matthew Meselson at
8556-428: 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'. 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 ,
8649-485: Was thought at first to be protection of the 3′ end of the RNA from nucleases, but later the specific roles of polyadenylation in nuclear export and translation were identified. The polymerases responsible for polyadenylation were first purified and characterized in the 1960s and 1970s, but the large number of accessory proteins that control this process were discovered only in the early 1990s. Messenger RNA In molecular biology , messenger ribonucleic acid ( mRNA )
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