RNA Processing Educational Materials

RNA Processing Overview of RNA Processing RNA is processed in many different ways In the simplest case, the ends of the transcript are removed from the larger precursor RNA by RNAcleaving enzymes called ribonucleases The coding sequence of many genes, particularly eukaryotic mRNAs, is not continuous but is interrupted by non-coding sequences known as introns. Despite their seemingly disruptive nature, introns are included in the precursor RNA produced by RNA polymerase, along with the coding segments or exons However, introns must be removed to generate a functional species so that, for example, an mRNA will be translated into a functional protein. The removal of the introns and rejoining of the exons that remain is known as RNA splicing Eukaryotic pre-mRNAs also undergo a modification known as 5' capping whereby the 5' end becomes modified with a 7-methylguanosine connected by an unusual linkage; they also undergo polyadenylation in which a long stretch of adenosine nucleotides is added to the 3' end as part of the transcription termination process RNA processing events are points for regulation and quality control, and are sources of diversity Fundamentally, RNA processing is required to produce functional RNAs, but processing also brings with it at least three associated benefits (1) processing events contribute to the regulation of gene expression; the efficiency with which a particular RNA is spliced, capped, polyadenylated, and edited governs how quickly the RNA can function or be translated In addition, the concentration of any RNA in a cell is regulated by the balance between the transcription of the RNA (the rate at which a given RNA is synthesized) and the degradation of the RNA by nucleuses (2) as well as providing a means for regulating gene expression levels, RNA processing can generate many different RNAs from just one gene Alternative splicing determines whether a given sequence is present or not in the final processed mRNA transcript; for exons that constitute the coding portion of an mRNA, an exon encodes an amino acid sequence that may or may not be included in a protein synthesized from the precursor RNA once splicing has occurred RNA editing, on the other hand, involves removing, inserting, or chemically modifying individual nucleotides, all events that can change the amino acid sequence of the encoded protein (3) RNA processing also serves as a quality control step In addition to these systems that monitor endogenous RNA quality, eukaryotic cells possess a mechanism referred to as RNA interference to detect and degrade foreign RNAs produced by parasites such as viruses Many RNA processing machines have RNA components In addition, many complexes are localized to specific compartment in eukaryotic cells; some RNA processing complexes are found in the nucleus, either distributed throughout or located to specific regions such as the nucleolus, whereas others are found in the cytoplasm Some RNAs have catalytic activity and are termed ribozymes. Others are called guide RNAs because they base-pair with the precursor RNAs and guide the catalytic components of an RNP to where the processing events should take place tRNA and rRNA Processing tRNAs and rRNAs are synthesized as longer precursors The transcripts for most tRNAs and rRNAs in all organisms are synthesized as long precursor molecules that must be processed to produce functionally active RNAs Synthesis of a single long precursor ensures that similar amounts of the functional RNAs, such as all three rRNAs, are produced, simply because the synthesis of one is intrinsically linked to another as they come from the same precursor molecule Some ribonucleases, denoted exonucleases, digest the RNA strand by successively removing nucleotides from the end Many exonucleases recognize the 3' end and digest in the 3' to 5' direction, although some bacterial and eukaryotic exonucleases begin digestion at the 5' end and proceed in the 3' direction Endonucleases differs in their specificities for RNA targets; some endonucleases cleave double-stranded RNA, while others cleave single-stranded RNA In general, the various processing steps do not occur in isolation, but instead are coordinated with each other and with other cellular processes The endonuclease RNase III cleaves and trims tRNA precursors Excision of the bacterial rRNAs from longer precursors and the trimming of some rRNAs and tRNAs are carried out by the endonuclease RNase III, which recognizes double-stranded RNA The RNA-containing endonuclease RNase P cleaves the 5’ ends of tRNAs The precise trimming of the 5’ end of tRNAs is accomplished by the endonuclease ribonuclease P (RNase P), which cleaves single-stranded RNA The RNA component of bacterial RNase P alone can act as an enzyme to cut the RNA and was one of the first RNAs shown to act as a ribozyme. The single protein subunit of the bacterial enzyme enhances performance relative to that achieved by the RNA component alone and may broaden the range of substrates the enzyme can cleave Several tRNAs and some rRNAs have introns that require silencing The precursor RNAs for several tRNAs and some rRNAs are interrupted by introns, which must be removed to produce the functional RNA; this removal provides an additional step for regulation and quality control In the cases of self-splicing, the precursor rRNAs themselves act as ribozymes that catalyze the removal of introns and the joining of the exons that remain (referred to as intron excision and exon ligation, respectively) CCA is added to tRNAs in the absence of a nucleic acid template The 3' termini of tRNAs contain a universally conserved CCA sequence, which is the site of attachment for the amino acid that the tRNA carries to the ribosome during protein synthesis For some bacterial tRNAs, this CCA sequence is encoded by the tRNA gene, but for most tRNAs, this sequence is added post-transcriptionally by a CCA-adding enzyme Although the CCA-adding enzyme shares sequence similarity with a DNA repair polymerase, the enzyme does not use a nucleic acid template to direct the addition of two C residues followed by a single A residue to the tRNA Both the size and shape of this binding pocket change, depending on the form of tRNA bound - the tRNA without the CCA tail, or the tRNA with a single added to the 3' end of the tRNA at each step, and hence drive the synthesis of the correct CCA tail tRNA and rRNA Nucleotide Modifications Nucleotides in tRNAs and rRNAs are modified in numerous ways Many of the nucleotides in tRNAs and rRNAs are chemically modified after transcription. The modifications can be found on the nucleotide base or the ribose sugar ring Typically, particular positions in different tRNA and rRNA species are specifically modified, and for those modifications that have been studied in detail, they often appear to be required for the optimal survival and growth of organisms Some of these modifications seem to contribute to the overall structural stability of tRNAs and to their ability to interact with other molecules It is thought that the extra hydrogen-bonding capacity of pseudouridine relative to uridine could allow this modified nucleotide to help stabilize the structure of the ribosome Specific enzymes catalyze individual tRNA and some rRNA modifications In bacteria, the modifications found on tRNAs and rRNAs are added by site-specific enzymes that catalyze a given modification at a specific site in the RNA Despite this, the large number and diversity of modifications and the large number of proteins that are committed to their synthesis indicate that these modifications must play a biologically significant role snoRNAs guide methylation and pseudouridylation of eukaryotic and archaeal rRNAs and some tRNAs Although the enzymes that carry out these modifications in all organisms are similar, the mechanism by which most sites are recognized in archaea and eukaryotes is very different from the mechanism found in bacteria The snoRNAs associate with specific sets of proteins, which include the enzyme that carries out the modification reaction, to form an RNP known as a snoRNP SnoRNAs range in length between 60 and 300 nucleotides and are found in the nucleolus where the majority of the ORNA processing occurs The snoRNAs fall into two major classes that possess distinct conserved sequence elements and direct different nucleotide modifications; the RNAs that direct ribose methylation are referred to as the box C/ D snoRNAs, and the RNAs that direct pseudouridylation are referred to as the box H/ACA snoRNAs The snoRNA within the RNP complex base-pairs with the target RNA and thus directs the modification enzymes to particular positions mRNA Capping and Polyadenylation Eukaryotic mRNAs are capped at the 5' end in a multistep process The 5' ends of the mRNAs are "capped" with a special 7-methylguanine nucleotide that is attached to the end of the message via a unique 5’-5’ triphosphate linkage This structure, called the 5' cap, is essential for the efficient elongation and termination of transcription, as well as the subsequent processing of the mRNA The cap structure also functions as a binding site for proteins that export the mRNA from the nucleus to the cytoplasm, and for directing the initiation of protein synthesis from the mRNA The 5' cap is added to eukaryotic mRNA in three successive steps that occur soon after the growing RNA emerges from RNA polymerase II, when only 20-30 nucleotides have been synthesized (1) an RNA 5' triphosphatase catalyzes the removal of one phosphate from the triphosphate at the 5' end of the mRNA (2) a guanyl transferase then attaches a molecule of guanosine monophosphate (GMP) (in reaction utilizing guanosine triphosphate (GTP)) to this end a 5'-5’ triphosphate linkage (3) the transferred guanine is methylated by a guanine-7-methyltransferase In higher eukaryotes, the 2' OH positions of ribose in the second and sometimes the third nucleotides of the mRNA are also methylated, which seems to allow more efficient translation of these mRNAs Eukaryotic mRNAs are polyadenylated at the 3' end The 3' ends of all eukaryotic mRNAs, except those encoding metazoan histones, are modified by the addition of a tail of adenosine residues (approximately 200 nucleotides in length in mammalian cells), called a polyadenosine (poly (A)) tail The process begins with an initial cleavage of the mRNA. For most transcripts, the cleavage occurs after a CA nucleotide pair that lies somewhere between a conserved AAUAAA hexamer sequence and a U- or GU-rich region further downstream In general, a larger complex of proteins is required for this sequence of reactions than is required for the 5' capping reactions; it is speculated that the larger complex is required because the polyadenylation enzymes must be able to perform the difficult job of recognizing and processing the different polyadenylation sites in different mRNAs These alternative polyadenylation sites (APAs) contribute to the regulation of protein synthesis and expand the range of protein products made from a single mRNA species mRNA stability and translation in eukaryotes are often regulated by factors, both proteins and regulatory RNAs, which bind to the 3' untranslated regions (UTRs) of a given mRNA The 3' ends of mRNAs encoding metazoan histones are not polyadenylated, but instead carry highly conserved stem-loop structures that engage specialized RNA-binding proteins with functions related to the proteins that bind the poly (A) tails Capping and polyadenylation are intimately coupled to each other, and to transcription, by RNA polymerase II There is an intimate association between 5' capping and 3' polyadenylation, and also with other processes that occurs during transcription by RNA polymerase II The region of RNA polymerase II that is responsible for orchestrating all of these mRNA processing events is the C - terminal domain (CTD) of RPB1, the largest subunit of the polymerase RNA polymerases I and III do not have a domain equivalent to the RPB1 CTD (of RNA polymerase II), and RNAs that are synthesized by these polymerases are not capped and polyadenylated Transcription and polyadenylation are also coupled to appropriate mRNA localization Although the transcription and processing of eukaryotic mRNAs occur in the nucleus, translation of mRNAs occurs in the cytoplasm. Thus, mRNAs must be exported out of the nucleus before translation can occur The downstream steps of mRNA export and translation are tightly linked to both transcription and processing of the mRNA; the protein factors required for nuclear export are loaded onto the precursor mRNA during transcription, but the export-component mRNA - protein complexes are not released from the transcription complex until they receive signals from polyadenylation enzymes Beyond merely being transported out of the nucleus, some mRNAs are localized to very specific regions of the cytoplasm, allowing synthesis of the encoded proteins in defined regions of the cell RNA Splicing Introns must be removed from precursor RNAs There are a number of different classes of introns, whose relative distribution and abundance depend on the kingdom in which they are found. Some are excised by proteins, some by RNPs, and some excise themselves Most introns do not themselves contain genes and are simply removed from the precursor RNAs and degraded. Exceptions to this rule are the snoRNAs and certain miRNAs in invertebrates and mammals, both of which are commonly found in the introns of mRNAs Indeed, the existence of introns has allowed for a process referred to as exon shuffling, wherein the DNA encoding exons can be exchanged and reordered through genetic recombination between intronic DNA sequences RNA splicing occurs by sequential transesterification reactions The two exons that surround an intron are not directly joined to one another in a single step. Instead, a two-step reaction occurs in which the intron is first detached from exon 1, freeing this exon to react with exon 2 Both of these reaction steps are transesterifications in which a single phosphodiester bond between two nucleotides is broken and replaced with an energetically equivalent phosphodiester bond The replacement of one chemical bond with a similar chemical bond has too implications - first, the reaction can occur without the het input of energy from an energy source such as ATP; and second, the reaction can be readily reversible Group I introns can be self-splicing Many group I introns are autocatalytic RNAs, or ribozymes, which can catalyze their own excision from a primary transcript in a splicing reaction involving two sequential transesterifications The first transesterification reaction has the unusual feature that a free guanosine nucleotide (rather than a specific nucleotide within the RNA molecule) is the attacking species that detaches the 5' end of the intron from its neighboring exon 1 In the second transesterification reaction, the released terminus of exon 1 attacks at the intron-exon 2 junction, thus joining the two exons together and releasing the free intron The splice sites are précises defined by the three-dimensional structure of the intron, and by the recognition of a conserved G-U wobble pairing interaction found within a paired helical region Group II introns splice via the same chemical mechanism as spliceosomal introns Group II introns are somewhat larger in size than their group I cousins (group I introns range from ~120 to 450 nucleotides in size and group II introns range from ~400 to 1000 nucleotides in length, excluding internal open reading frames, and they perform a slightly different set of transesterification reactions As was true for group I introns, the splice sites of group II introns are defined by the three-dimensional structure of the intron itself and by specific base-parings and tertiary interactions between intron and exon segments that position the critical sites within the catalytic center of the ribosome Group II introns are also interesting in that they can act as mobile genetic elements that attack and insert themselves into duplex DNA by a reversal of the splicing mechanism Eukaryotic mRNA Splicing by the Spliceosome Splicing of eukaryotic mRNAs is carried out by a large RNP machine called the spliceosome The vast majority of eukaryotic introns are not self-splicing, and the formidable task of identifying and splicing together exons among all the intronic RNA is performed by a large ribonucleoprotein machine, the spliceosome The spliceosome is composed of several individual small nuclear ribonucleoproteins (snRNPs), pronounced "snurps", which comprise both RNA and protein components and many more additional proteins that come and go during the splicing reaction In both cases, the 2' OH of an adenosine residue located within the intron itself attacks the exon 1-intron boundary, detaching the intron from the exon and producing a branched intron structure (the lariat) The high similarity in mechanism between the transesterification reactions catalyzed by the group II intron and the spliceosome has led to the idea that the simpler self-splicing intron is the evolutionary predecessor of the more complicated multicomponent eukaryotic machinery Splice site recognition and spliceosome assembly are dominated by RNA-RNA interactions Before splicing can occur, the spliceosome must identify the splice sites - the sites at which exons are separated from their neighboring introns and at which two exons are subsequently attached Key sequences are the 5' and 3' splice sites, a branch-point nucleotide within the intron, and a polypyrimidine tract before the 3' splice site These additional sequence determinants allow cells to produce different mature RNAs from a precursor RNA, depending on which introns and exons are utilized by spliceosomes The spliceosome is composed of five snRNPs (U1, U2, U4, U5, and U6), each containing an RNA molecule called a small nuclear RNA (snRNA) that is usually 100 - 300 nucleotides long and several protein factors Other protein factors recognize specific sequences in the mRNA or promote the conformational rearrangements in the spliceosome that are required for the splicing reaction to progress The 5' splice site is recognized by the U1 snRNP. Other splice site consensus sequences are recognized by non-snRNP factors; the branch-point sequence is recognized by the branch-point-binding protein (BBP), and in metazoans, the polypyrimidine tract and 3' splice site are bound by two specific protein components of a splicing complex referred to as U2AF Following the binding of these initial components, the remainder of the splicing apparatus assembles around them, in some cases displacing some of the previously bound components Other rearrangements in the spliceosome next bring together the newly freed exon 1 and the intron-exon 2 junction - the two RNA pieces that will be joined to create the final mRNA product - and the second transesterification reaction completes the splicing Protein factors contribute in multiple ways to pre-mRNA splicing In addition to the snRNPs and proteins we have already mentioned, there are hundreds of other proteins that are associated with the splicing machinery and play important roles in the process A number of ATPases facilitate structural rearrangements of the snRNAs during the sequential splicing steps, as well as promote mRNA and intron lariat release after the reaction is complete Mis-splicing in the cell can have dire consequences, as the desired product is not produced and often the wrong products can be toxic for the men. Such as an expenditure of energy for the purpose of promoting fidelity is a common feature of biological reactions For example, the SR proteins (named after the serine (S)/arginine (R) dipeptide repeats that they possess) bind to the pre-mRNA where they recruit other components of the spliceosome to the 5' and 3' splice sites SR proteins can be heavily modified by phosphorylation on their abundant serine residues, and the extent of this phosphorylation may be altered throughout the splicing cycle to modulate splicing events Extensive study of the human spliceosome has shown that some of its integral components are also involved in transcription, polyadenylation, nuclear mRNA export, and translation, broadly highlighting the intimate coordination of biochemical events in mRNA biogenesis The process of splicing leaves behind a set of proteins, the exon junction complex (EJC), at splice junctions, this "marking" the transcript as processed and ready for export and translation These EJCs are eventually recognized by the translational machinery in a process that evaluates whether the mRNA represents a full-length product (a form of quality control) or should instead be targeted for decay High-resolution cryoEM structures are providing new information about the spliceosome mechanism Importantly, it is clear that the spliceosome is a dynamic ribonucleoprotein machine and that conformational changes in the RNA components themselves are central to the spliceosomes function Indeed, the known ATP dependence of the splicing reaction is thought, in part, to reflect the requirements of the many helicases that promote and regulate these RNA-based conformational rearrangements A minority of genes in animals and plants are processed by an alternative set of splicing snRNPs (the AT-AC spliceosome) While the majority of pre-mRNA introns have GU and AG dinucleotides at their termini and are recognized by the “major” spliceosome described earlier, some introns in multicellular organisms are processed by a splice some that includes the same U5 component as described previously, but four different snRNPs (U11, U12, U4atac, and U6atac) Trans splicing joins exons from two separate RNA transcripts The different splicing processes described earlier are all examples of cis splicing - that is, the splicing events occur between parts of the same molecule. Another unusual form of splicing is trans splicing, which results in exons from two separate RNA molecules becoming joined together Following the trans splicing reaction, the SL RNA represents the first exon in the mature mRNA and is typically located just upstream of the AUG initiation site During the trans splicing reaction, the SL RNA is bound to proteins to form the SL snRNP, effectively replacing the U1 snRNP bound to the 5' splice site during the more standard splicing reactions Exon Definition and Alternative Splicing Diversity in gene expression in eukaryotes derives from alternative splicing In a gene comprising multiple introns and exons, the process of splicing may yield more than just a single mature mRNA in which the exons are joined in only one way Instead, as many as 95% of genes in higher eukaryotes undergo alternative splicing, in which different combinations of exons in a gene are spliced together to produce different mature mRNAs Although most exons are constitutive, meaning that they are always included in the final mRNA, regulated exons that may or may not be included are also common In addition to the potential exclusion or inclusion of a particular exon, the splicing pattern of an mRNA can be altered by the utilization of alternative 5' or 3' splice sites What alternative splicing occurs depends on a variety of factors such as the cell type, the developmental stage of the cell or organism, or cues from the cellular environment, and are typically mediated through interactions with a large group of auxiliary proteins involved in the splicing reactions that we will describe later Exon and intron definition models help to explain how the ordered recognition of splice sites can occur The sequences that define the exon-intron junctions are, as we have seen, relatively simple. Consequently, similar sequences commonly occur in introns purely by chance; such accidental splicing signals are known as cryptic splice sites There are two broad conceptual models for how the spliceosome correctly identifies splice sites. These models are called exon definition and intron definition Exon definition: the hypothesis that exons, rather than introns, are defined by proteins that bind to the exon sequence and by interactions between the 3' and 5' splice site spliceosome components across the defined exon Intron definition: hypothesis that introns, rather than exons, are defined through interactions between sequential 5' and 3' splice site bound factors This hypothesis nicely explains several general observations from mammalian splicing systems - that exons tend to be short relative to introns and thus simpler to define, and that mutation of 5' splice sites tends to result in exon exclusion rather than intron inclusion While both models help us to understand how sequential splice sites are identified to promote ordered and accurate splicing, it is clear that the final active splicing complex must be one in which 5' and 3' splice site protein complexes interact with one another across the intron (to facilitate its removal) Co-transcriptional splicing allows sequential splice sites to "see" one another as they emerge from the polymerase, thus minimizing the chance that distant exons are mistakenly joined together Alternative splicing is regulated by a complex set of pre-mRNA sequences in exons and introns that are recognized by diverse cellular factors However, the splice site consensus sequences do not provide sufficient information to determine whether a site will be identified as functional by the spliceosome Moreover, the selection of particular splice sites is often tightly regulated in order to include or omit specific exons, or portions of them, from the mature mRNA RNA elements that positively affect splicing are referred to as enhancers. Such intronic and exonic splicing enhancer sequences (ISE and ESE, respectively) typically bind proteins that increase the ability of spliceosomes to identify nearby splice sites in a pre-mRNA Intronic and exonic splicing silencer sequences (ISS and ESS, respectively) have the opposite effect, often masking splice sites or blocking spliceosome assembly, thus causing exons to be omitted from the mature mRNA In non-neuronal cells, inclusion of the N1 exon is repressed by the PTB protein bound to intronic silencer elements on both sides of the exon RNA Editing mRNAs can be edited by the modification, insertion, and deletion of specific nucleotides This editing can affect only one or two nucleotides (akin to the correction of a few typographical errors) or it can be surprisingly extensive (akin to the complete rewriting of a text); it can involve as many as half of the nucleotides in the mRNA Editing is another way for a cell to vary the amino acid sequence of a protein that is encoded by a given mRNA and makes it extremely difficult for us to predict the protein sequence encoded by a gene whose precursor RNA is processed in this way Widespread forms of editing are the deamination of adenosine to form inosine, the deamination of cytidine to form uridine, and the methylation of adenosine Adenosine deaminases that act on RNA convert adenosine to inosine The deamination of adenosine to inosine is one of the most widespread forms of mRNA editing in higher eukaryotes and can occur in coding sequences, introns, and the 5' and 3' UTR of transcripts Consequently, changes of this type within coding regions generally result in changes in the sequence of the protein translated from the mRNA Interestingly, ADARs deaminate as many as half of the adenosines in some RNAs, while in others, they target a specific adenosine among hundreds Uridine addition and deletion are directed by guide RNAs The guide RNAs are partially complementary to the unedited RNA but are more extensively complementary to the fully edited mRNA During each editing step, an endonuclease cuts the mRNA at a mismatch between the guide RNA and mRNA, and the guide RNA then serves as a template to direct the addition or deletion of uridines The final step in both the addition and deletion steps of uridine editing is the ligation of the resulting edited fragments of the mRNA Degradation of Normal RNAs RNA degradation can influence gene expression All cells have mechanisms to degrade Ram, digesting the RNA into individual nucleotides. This degradation allows cells to remove RNAs that are no longer required or which might be present at too high a level for the current needs of the cell Cells have methods to degrade "normal" RNAs - those RNAs that perform useful functions to cells - and often different methods to efficiently destroy foreign or defective RNAs Some RNAs, such as rRNAs and tRNAs, are needed for long periods of time and comparatively stable. In contrast, other RNAs, such as some mRNAs, are only needed briefly and are rapidly degrade A variety of determinants impact RNA stability On the other hand, the presence of a poly (A) tail in bacteria is associated with decreased stability. By contrast, in eukaryotes, the poly (A) tail generally tends increased stability to RNA transcripts, whereas other elements, including the AU-rich elements (AREs) found in the 3' UTRs of some mRNAs, cause instability by directing poly (A) tail removes When these viruses infect a host cell, the absence of an ARE prevents the v-fos mRNA from being rapidly degraded, leading to high levels of the v-fos protein, which promotes the uncontrolled growth of infected cells In all organisms, processes that act on RNAs - such as RNA splicing, transport of the RNA through cellular compartments, or the translation of an mRNA into protein - also impact RNA half-life RNA degradation in eukaryotes and bacteria involves multiple steps Although the degradation processes for bacterial and eukaryotic RNAs were originally thought to be distinct, the discovery of an increasing number of common degradation machinery components points to some similarity between the two pathways The products of the initial endonuclease digestion are then degraded by 3' to 5’ exonucleases. Most often, the initiating endonuclease is RNase E, which is part of a protein complex called the degradosome The degradosome contains a number of proteins likely to facilitate degradation, including an RNA helicase that uncoils double-stranded regions of the RNA and a 3' to 5' exonuclease denoted polynucleotide phosphorylase (PNPase) However, RNA stem-loop structures can block the accessibility of the 3' end, making RNAs resistant to exonuclease action. The digestion of such RNAs is facilitated by polyadenylation of the 3' ends, which provides an accessible, unstructured end for the action of exonucleases In eukaryotes, RNA degradation generally is not initiated by the action of endonucleases. Instead, mRNA decay involves a series of exonucleolytic digestions Committing an mRNA to decay after deadenylation involves one of two distinct mechanisms - the mRNA can be destroyed from either the 5' or the 3' end Degradation of RNAs can be regulated in response to specific signals The steps in the degradation of RNAs can all be promoted or blocked in response to specific environmental signals, at different points in the cell cycle, in different cell types, or in different stages of development The mRNA encoding the transferrin receptor is rapidly degraded by nucleuses when iron levels in a cell are high and the cell has no need to import more iron. However, when iron levels are low, the transferrin receptor mRNA is protected from degradation Specific stress signals can lead to more general to degradation of RNAs Sometimes, under conditions of starvation or extreme stress, it might be advantageous to the cell to degrade a large proportion of RNA molecules in a last-ditch effort to scavenge nucleotides and survive Degradation of Foreign and Defective RNAs Foreign and defective RNAs can be harmful to cells For example, "foreign" RNAs, derived from sources such as viruses or transposons, can be detrimental to the cell if the RNAs are translated into proteins that inhibit critical cell functions or promote transposition In addition, an RNA that is defective in some way, due to errors during transcription or RNA processing, has the potential to disrupt normal cellular processes by encoding a product with altered function Foreign RNAs are removed by a RNAi mechanism in eukaryotes and CRISPR systems in bacteria The RNA molecules derived from transcription of many viruses that enter eukaryotic cells or from the transcription of transposons or other repetitive sequences in the chromosome are typically doublestranded This defense system was denoted CRISPR, based on the first evidence for this system - clustered regularly interspaced short palindromic repeats identified by genome sequencing Defective mRNAs are recognized and removed by specific decay mechanisms However, some defective mRNAs contain a premature translation termination codon that causes the ribosome to stop synthesis before the natural protein is completed; others completely lack a termination codon that prevents the termination reaction from occurring, while still others have problematic coding sequences that can promote stalling during translation In bacterial cells, ribosomes stalled on the mRNAs - and particularly truncated mRNAs lacking stop codons - are recognized by A unique RNA that functions as both a tRNA and an mRNA