The general structural characteristics of ribosomes are discussed in Chapter 34. These particulate entities serve as the machinery on which the mRNA nucleotide sequence is translated into the sequence of amino acids of the specified protein. The translation of the mRNA commences near its 5′ end with the formation of the corresponding amino terminus of the protein molecule. The message is decoded from 5′ to 3′, concluding with the formation of the carboxyl terminus of the protein. Again, the concept of polarity is apparent. As described in Chapter 36, the transcription of a gene into the corresponding mRNA or its precursor first forms the 5′ end of the RNA molecule. In prokaryotes, this allows for the beginning of mRNA translation before the transcription of the gene is completed. In eukaryotic organisms, the process of transcription is a nuclear one, while mRNA translation occurs in the cytoplasm, precluding simultaneous transcription and translation in eukaryotic organisms and enabling the processing necessary to generate mature mRNA from the primary transcript.

Initiation Involves Several Protein-RNA Complexes

 Initiation of eukaryotic protein synthesis requires that an mRNA molecule be selected for translation by a ribosome (Figure 1). Once the mRNA binds to the ribosome, the ribosome must locate the initiation codon thereby setting the correct reading frame on the mRNA, and translation begins. This process involves tRNA, rRNA, mRNA, and at least 10 eukaryotic initiation factors (eIFs), some of which have multiple (three to eight) subunits. Also involved are GTP, ATP, and amino acids. Initiation can be divided into three steps, all of which are obligatorily preceded by dissociation of the 80S ribosome into its constituent 40S and 80S subunits: (1) binding of a ternary complex consisting of the initiator methionyl-tRNA (met-tRNAi), GTP, and eIF-2 to the 40S ribosome to form the 43S preinitiation complex; (2) binding of mRNA to the 40S preinitiation complex to form the 48S initiation complex; and (3) combination of the 48S initiation complex with the 60S ribosomal sub unit to form the 80S initiation complex.

Fig1, Diagrammatic representation of the initiation phase of protein synthesis on a eukaryotic mRNA. Eukaryotic mRNAs contain a 5′ 7meG-cap (Cap) and 3′poly(A) terminal [(A)n ] as shown. Translation preinitiation complex formation proceeds in several steps: (1) Dissociation of the 80S complex to component 40S and 60S subunits, a process facilitated by binding of factors eIF1, eIF1A, and eIF3 to the ribosomal 40S subunit (top). (2) Formation of the 43S preinitiation complex, a ternary complex consisting of met-tRNAi and GTP-bound to the initiation factor eIF-2 (eIF-2-GTP; left). This complex is then bound by the eIF5 initiation factor forming the complete 43S preinitiation complex. (3) Activation of 5′-capped mRNA and formation of the 48S initiation complex. mRNA is bound via its 5′-cap by eIF4F (composed of eIF4E, eIF4G, and eIF4A factors) and 3′ Poly(A) tail by Poly A binding (PAB) protein forming the 48S initiation complex. ATP hydrolysis-dependent 5′ to 3′ mRNA scanning enables location of the initiation codon AUG, which is then bound by met-tRNAi . (4) Following addition of GTP-bound eI5B and dissociation of eIF1, eIF2-GDP, eIF3, and eIF5, formation of the 80S initiation complex occurs when a recycled 60S ribosomal subunit joins the 48S complex. This reaction positions the initiator met-tRNAi within the P-Site of the active 80S initiation complex formation induces dissociation of eIF1A and GDP-bound eIF5B (see text for details).This complex is now competent for translation initiation. (GTP, •; GDP, °); the various initiation factors appear in abbreviated form as circles or squares, for example, eIF-3, (➂), eIF-4F, (4F), ( ). 4•F is a complex consisting of 4E and 4A bound to 4G (see Figure 2). Note that the “circular” structure of mRNA illustrated in Figure 2 is thought to be the actual form of mRNA on which steps 1 to 4 actually occur.

Ribosomal Dissociation

 Prior to initiation, 80S ribosomes dissociate into component 40S and 60S subunits during translation termination (see following discussion). Dissociation allows these components to participate in subsequent rounds of translation. Two initiation factors, eIF-3, eIF-1, and eIF-1A, bind to the newly dissociated 40S ribosomal subunit. Binding of these three eIFs delay reassociation of the 40S subunit with the 60S subunit, allowing other translation initiation factors to associate with the 40S subunit.

Formation of the 43S Preinitiation Complex

 The first step of translation initiation involves the binding of GTP by eIF-2. This binary complex then binds to methionyl tRNAi, a tRNA specifically involved in binding to the initiation codon AUG. It is important to note that there are two tRNAs for methionine. One specifies methionine for the initiator codon, the other for internal methionines. Each has a unique nucleotide sequence; both are aminoacylated by the same methionyl-tRNA synthetase. The GTP-eIF-2-tRNAi ternary complex binds to the 40S ribosomal subunit to form the 43S preinitiation complex. The ternary complex–40S subunit complex is stabilized by eIF-3 and eIF-1A and the subsequent binding of eIF5.

eIF-2 is one of two control points for protein synthesis ini tiation in eukaryotic cells. eIF-2 consists of α, β, and γ subunits. eIF-2α is phosphorylated (on serine 51) by at least four different protein kinases (HCR, PKR, PERK, and GCN2) that are activated when a cell is under stress and when the energy expenditure required for protein synthesis would be deleterious. Such conditions include amino acid or glucose starvation, virus infection, intracellular presence of large quantities of misfolded proteins (endoplasmic reticulum [ER] stress), serum deprivation (for cells in culture), hyperosmolality, and heat shock. PKR is particularly interesting in this regard. This kinase is activated by viruses and provides a host defense mechanism that decreases protein synthesis, including viral protein synthesis, thereby inhibiting viral replication. Phosphorylated eIF-2α binds tightly to and inactivates the GTP–GDP recycling protein eIF-2B, thus preventing formation of the 43S preinitiation complex and blocking protein synthesis.

Formation of the 48S Initiation Complex

As described in Chapter 36, the 5′ termini of mRNA molecules in eukaryotic cells are “capped.” The 7meG-cap facilitates the binding of mRNA to the 43S preinitiation complex. A cap binding protein complex, eIF-4F (4F), which consists of eIF-4E (4E)and theeIF-4G (4G)-eIF-4A (4A) complex, binds to the cap through the 4E protein. Subsequently eIF-4B (4B) binds and reduces the complex secondary structure of the 5′ end of the mRNA through its ATP-dependent helicase activity. The association of mRNA with the 43S preinitiation complex to form the 48S initiation complex requires ATP hydrolysis. eIF-3 is a key protein because it binds with high affinity to the 4G component of 4F, and links this complex to the 40S ribosomal subunit. Following association of the 43S preinitiation complex with the mRNA cap, and reduction (“melting”) of the secondary structure near the 5′ end of the mRNA through the action of the 4B helicase and ATP, the complex translocates 5′ → 3′ and scans the mRNA for a suitable initiation codon. Generally, this is the 5′-most AUG, but the precise initiation codon is determined by so-called Kozak consensus sequences that surround the AUG initiation codon:

Role of the Poly(A) Tail in Initiation

 Biochemical and genetic experiments have revealed that the 3′ poly(A) tail and the poly(A) binding protein, PAB, are both required for efficient initiation of protein synthesis. Further studies showed that the poly(A) tail stimulates recruitment of the 40S ribosomal subunit to the mRNA through a complex set of interactions. PAB (Figure 2) bound to the poly(A) tail, interacts with eIF-4G, and 4E subunits of cap bound eIF-4F to form a circular structure that helps direct the 40S ribosomal subunit to the 5′ end of the mRNA and also likely stabilizes mRNAs from exonucleolytic degradation. This helps explain how the cap and poly(A) tail structures have a synergistic effect on protein synthesis. Indeed, differential protein–protein interactions between general and specific mRNA translational repressors and eIF-4E result in m7G cap dependent translation control (Figure 3).

Fig2. Schematic illustrating the circularization of mRNA through protein–protein interactions between 7meG cap-bound elF4F and poly(A) tail-bound poly(A) binding protein. elF4F, composed of elF4A, 4E, and 4G subunits binds the mRNA 5′-7meG “Cap” (7meGpppX-) upstream of the translation initiation codon (AUG) with high affinity. The elF4G subunit of the complex also binds poly(A) binding protein (PAB) with high affinity. Since PAB is bound tightly to the mRNA 3′-poly(A) tail (5′-(X)n A(A)n AAAAAAAOH 3′), circularization results. Shown are multiple 80S ribosomes that are in the process of translating the circularized mRNA into protein (black curlicues), forming a polysome. On encountering a termination codon (here UAA), translation termination occurs leading to release of the newly translated protein and dissociation of the 80S ribosome into 60S, 40S subunits. Dissociated ribosomal subunits can recycle through another round of translation (see Figures 1 and 5).

Fig3. Activation of eIF-4E by insulin and formation of the cap-binding eIF-4F complex. The 4F-cap mRNA complex is depicted as in Figures 1 and 2. The 4F complex consists of eIF-4E (4E), eIF-4A (4A), and eIF-4G (4G). 4E is inactive when bound by one of a family of binding proteins (4E-BPs). Insulin and mitogenic growth polypeptides, or growth factors (eg, IGF-1, PDGF, interleukin-2, and angiotensin II) activate the PI3 kinase/AKT kinase signaling pathways, which activate the mTOR kinase; this results in the phosphorylation of 4E-BP . Phosphorylated 4E-BP dissociates from 4E, and the latter is then able to form the 4F complex and bind to the mRNA cap. These growth polypeptides also induce phosphorylation of 4G itself by the mTOR and MAP kinase pathways. Phosphorylated 4F binds much more avidly to the cap than does nonphosphorylated 4F, which stimulates 48S initiation complex formation and hence translation.

Formation of the 80S Initiation Complex

The binding of the 60S ribosomal subunit to the 48S initiation complex involves hydrolysis of the GTP bound to eIF-2 byeIF-5. This reaction results in release of the initiation factors bound to the 48S initiation complex (these factors then are recycled) and the rapid association of the 40S and 60S subunits to form the 80S ribosome. At this point, the met-tRNAi is on the P site of the ribosome, ready for the elongation cycle to commence.

The Regulation of eIF-4E Controls the Rate of Initiation The 4F complex is particularly important in controlling the rate of protein translation. As described earlier, 4F is a complex consisting of 4E, which binds to the m7G cap structure at the 5′ end of the mRNA, and 4G, which serves as a scaffolding protein. In addition to binding 4E, 4G binds to eIF-3, which links the complex to the 40S ribosomal subunit. It also binds 4A and 4B, the ATPase helicase complex that helps unwind the RNA (see Figure 3).

4E is responsible for recognition of the mRNA cap structure, a rate-limiting step in translation. This process is further regulated by phosphorylation (see Figure 3). Insulin and mitogenic growth factors result in the phosphorylation of 4E on Ser209 (or Thr210). Phosphorylated 4E binds to the cap much more avidly than does the nonphosphorylated form, thus enhancing the rate of initiation. Components of the MAP kinase, PI3K, mTOR, RAS, and S6 kinase signaling pathways can all, under appropriate conditions, be involved in these regulatory phosphorylation reactions.

The activity of 4E is modulated in a second way, and this also involves phosphorylation; a set of proteins bind to and inactivate 4E. These proteins include 4E-BP1 (BP1, also known as PHAS-1) and the closely related proteins 4E-BP2 and 4E-BP3. BP1 binds with high affinity to 4E. The 4E-BP1 association pre vents 4E from binding to 4G (to form 4F). Since this interaction is essential for the binding of 4F to the ribosomal 40S subunit and for correctly positioning it on the capped mRNA, BP-1 effectively inhibits translation initiation.

Insulin and other growth factors result in the phosphorylation of BP-1 at seven unique sites. Phosphorylation of BP-1 results in its dissociation from 4E, and it cannot rebind until critical sites are dephosphorylated. These effects on the activation of 4E explain in part how insulin causes a marked post transcriptional increase of protein synthesis in liver, adipose, and muscle tissue.

Elongation Is Also a Multistep, Accessory Factor-Facilitated Process Elongation is a cyclic process on the ribosome in which one amino acid at a time is added to the nascent peptide chain (Figure 4). The peptide sequence is determined by the order of the codons in the mRNA. Elongation involves several steps catalyzed by proteins called elongation factors (EFs). These steps are (1) binding of aminoacyl-tRNA to the A site, (2) peptide bond formation, (3) translocation of the ribosome on the mRNA, and (4) expulsion of the deacylated tRNA from the P- and E-sites.

Fig4. Diagrammatic representation of the peptide elongation process of protein synthesis. The small circles labeled n − 1, n, n + 1, etc., represent the amino acid residues of the newly formed protein molecule (in N-terminal to C-terminal orientation) and the corresponding codons in the mRNA. EFIA and EF2 represent elongation factors 1 and 2, respectively. The peptidyl-tRNA, amino acyl-tRNA, and exit sites on the ribosome are represented by P site, A site, and E site, respectively.

Binding of Aminoacyl-tRNA to the A Site

In the complete 80S ribosome formed during the process of initiation, both the A site (aminoacyl or acceptor site) and E site (deacylated tRNA exit site) are free (see Figure 1). The binding of the appropriate aminoacyl-tRNA in the A site requires proper codon recognition. Elongation factor 1A (EF1A) forms a ternary complex with GTP and the entering aminoacyl-tRNA (see Figure 4). This complex then allows the correct aminoacyl tRNA to enter the A site with the release of EF1A-GDP and phosphate. GTP hydrolysis is catalyzed by an active site on the ribosome; hydrolysis induces a conformational change in the ribosome concomitantly increasing affinity for the tRNA. As shown in Figure 4, EF1A-GDP then recycles to EF1A GTP with the aid of other soluble protein factors and GTP.

Peptide Bond Formation

The α-amino group of the new aminoacyl-tRNA in the A site carries out a nucleophilic attack on the esterified carboxyl group of the peptidyl-tRNA occupying the P site (peptidyl or polypeptide site). At initiation, this site is occupied by the initiator met-tRNAi. This reaction is catalyzed by a peptidyl transferase, a component of the 28S RNA of the 60S ribosomal subunit. This is another example of ribozyme activity and indicates an important—and previously unsuspected— direct role for RNA in protein synthesis (Table 1). Because the amino acid on the aminoacyl-tRNA is already “activated,” no further energy source is required for this reaction. The reaction results in attachment of the growing peptide chain to the tRNA in the A site.

Table1. Evidence That rRNA Is a Peptidyl Transferase

Translocation.

The now deacylated tRNA is attached by its anticodon to the P site at one end and by its open 3′ CCA tail to the E site on the large ribosomal subunit (middle portion of Figure 4). At this point, elongation factor 2 (EF2) binds to and displaces the peptidyl tRNA from the A site to the P site. In turn, the deacylated tRNA is on the E site, from which it leaves the ribosome. The EF2-GTP complex is hydrolyzed to EF2-GDP, effectively moving the mRNA forward by one codon and leaving the A site open for occupancy by another ternary complex of amino acid tRNA–EF1A-GTP and another cycle of elongation.

The charging of the tRNA molecule with the aminoacyl moiety requires the hydrolysis of an ATP to an AMP, equivalent to the hydrolysis of two ATPs to two ADPs and phosphates. The entry of the aminoacyl-tRNA into the A site results in the hydrolysis of one GTP to GDP. Translocation of the newly formed peptidyl-tRNA in the A site into the P site by EF2 similarly results in hydrolysis of GTP to GDP and phosphate. Thus, the energy requirements for the formation of one peptide bond include the equivalent of the hydrolysis of two ATP molecules to ADP and of two GTP molecules to GDP, or the hydrolysis of four high-energy phosphate bonds. A eukaryotic ribosome can incorporate as many as six amino acids per second; prokaryotic ribosomes incorporate as many as 18 per second. Thus, the energy requiring process of peptide synthesis occurs with great speed and accuracy until a termination codon is reached.

Termination Occurs When a Stop Codon Is Recognized

In comparison to initiation and elongation, termination is a relatively simple process (Figure 5). After multiple cycles of elongation culminating in polymerization of the specific amino acids into a protein molecule, the stop or terminating codon of mRNA (UAA, UAG, UGA) appears in the A site. Normally, there is no tRNA with an anticodon capable of recognizing such a termination signal. Releasing factor 1 (RF1) recognizes that a stop codon resides in the A site (see Figure 5). RF1 is bound by a complex consisting of releasing factor 3 (RF3) with bound GTP. This complex, with the peptidyl transferase, promotes hydrolysis of the bond between the peptide and the tRNA occupying the P site. Thus, a water molecule rather than an amino acid is added. This hydrolysis releases the protein and the tRNA from the P site. On hydrolysis and release, the 80S ribosome dissociates into its 40S and 60S subunits, which are then recycled (see Figure 2). Therefore, the releasing factors are proteins that hydrolyze the peptidyl-tRNA bond when a stop codon occupies the A site. The mRNA is then released from the ribosome, which dissociates into its component 40S and 60S subunits, and another cycle can be repeated (see Figure 1).

Fig5. Diagrammatic representation of the termination process of protein synthesis. The 60S ribosomal peptidyl-tRNA, aminoacyl-tRNA, and exit sites are indicated as P site, A site, and E site, respectively. The termination (stop) codon is indicated by the three vertical bars and STOP. Releasing factor RF1 binds to the stop codon in the A site. Releasing factor RF3, with bound GTP, binds to RF1. Hydrolysis of the peptidyl-tRNA complex is shown by the entry of water (H2O); arrow. N and C indicate the amino- and carboxy-terminal amino acids of the nascent polypeptide chain, respectively, and illustrate the polarity of protein synthesis. Termination results in release of the mRNA, the newly synthesized protein (N- and C-termini; N, C), free tRNA, 40S and 60S subunits, as well as RF1, GDP-bound RF3, and inorganic Pi , as shown at bottom.

Polysomes Are Assemblies of Ribosomes

Many ribosomes can translate the same mRNA molecule simultaneously. Because of their relatively large size, the ribosome particles cannot attach to an mRNA any closer than 35 nucleotides apart. Multiple ribosomes on the same mRNA molecule form a polyribosome, or “polysome” (see Figure 2). In an unrestricted system, the number of ribosomes attached to an mRNA (and thus the size of polyribosomes) correlates positively with the length of the mRNA molecule.

Polyribosomes actively synthesizing proteins can exist as free particles in the cellular cytoplasm or may be attached to sheets of membranous cytoplasmic structures referred to as theendoplasmic reticulum (ER). Attachment of the particulate polyribosomes to the ER is responsible for its “rough” appearance as seen by electron microscopy. The proteins synthesized by the attached polyribosomes are extruded into the cisternal space between the sheets of rough ER and are exported from there. Some of the protein products of the rough ER are packaged by the Golgi apparatus for eventual export. The polyribosomal particles free in the cytosol are responsible for the synthesis of proteins required for intracellular functions.

Nontranslating mRNAs Can Form Ribonucleoprotein Particles That Accumulate in Cytoplasmic Organelles Termed P Bodies or Stress Granules

mRNAs, bound by specific packaging proteins and exported from the nucleus as ribonucleoproteins particles (mRNPs) sometimes do not immediately associate with ribosomes to be translated. Alternatively, under certain conditions where translation is slowed or stopped (cellular stress or developmental cues among other signals/conditions) select, untranslated mRNAs can associate with a range of specific RNAs and proteins to form P bodies and the related stress granules (SG). These structures are biomolecular condensates composed of interacting RNAs and proteins. P bodies can readily be visualized via immunohistochemistry using appropriate antibodies (Figure 6). These cytoplasmic structures are related to similar small mRNA-containing granules found in neurons and certain maternal cells. Overall P bodies (and SGs) are thought to contribute importantly to mRNA metabolism. Over 35 distinct proteins have been suggested to reside exclusively or extensively within P bodies. These proteins range from mRNA binding proteins to mRNA decapping enzymes, RNA helicases, and RNA exonucleases (5′-3′ and 3′-5′), to components involved in miRNA function and mRNA quality control. Incorporation of an mRNA into such complexes is not an unequivocal “death sentence.” Indeed, though the mechanisms are not yet fully understood, certain mRNAs appear to be temporarily stored in P bodies (or SGs) and then retrieved and utilized for protein translation. This molecular behavior suggests that the cytoplasmic functions of mRNA (translation and degradation) are controlled, at least in part, by the dynamic interaction of mRNA with polysomes and P body/SG protein/enzyme constituents.

Fig6. The P body is a cytoplasmic structure involved in mRNA metabolism. Shown is a photomicrograph of two mammalian cells in which a single distinct protein constituent of the P body has been visualized using the cognate-specific fluorescently labeled antibody. P bodies appear as small red circles of varying size throughout the cytoplasm. The cell plasma membranes are indicated by a solid white line, nuclei by a dashed line. Nuclei were counter stained using a fluorescent dye with different fluorescence excitation/ emission spectra from the labeled antibody used to identify P bodies; the nuclear stain intercalates between the DNA base pairs and appears as blue/green. Modified from http://www.mcb.arizona.edu/parker/ WHAT/what.htm. (Reproduced with permission from Dr. Roy Parker.)

The Machinery of Protein Synthesis Can Respond to Environmental Threats

 Ferritin, an iron-binding protein, prevents ionized iron (Fe2+) from reaching toxic levels within cells. Elemental iron stimulates ferritin synthesis by causing the release of a cytoplasmic protein that binds to a specific region in the 5′ nontranslated region of ferritin mRNA. Disruption of this protein-mRNA interaction activates ferritin mRNA and results in its translation. This mechanism provides for rapid control of the synthesis of a protein that sequesters Fe2+, a potentially toxic molecule. Similarly, environmental stress and starvation inhibit the positive roles of mTOR on promoting activation of eIF-4F and 48S com plex formation.

Many Viruses Co-opt the Host Cell Protein Synthesis Machinery

The protein synthesis machinery can also be modified in deleterious ways. Viruses replicate by using host cell processes, including those involved in protein synthesis. Some viral mRNAs are translated much more efficiently than those of the host cell (eg, encephalomyocarditis virus). Others, such as reovirus and vesicular stomatitis virus, replicate efficiently, and thus their very abundant mRNAs have a competitive advantage over host cell mRNAs for limited translation factors. Other viruses inhibit host cell protein synthesis by preventing the association of mRNA with the 40S ribosome.

Poliovirus and other picornaviruses gain a selective advantage by disrupting the function of the 4F complex. The mRNAs of these viruses do not have a cap structure to direct the binding of the 40S ribosomal subunit (see earlier). Instead, the 40S ribosomal subunit contacts an internal ribosomal entry site (IRES)in a reaction that requires 4G but not 4E. The virus gains a selective advantage by having a protease that attacks 4G and removes the amino terminal 4E binding site. Now the 4E-4G complex (4F) cannot form, so the 40S ribosomal subunit cannot be directed to host capped mRNAs, abolishing host cell protein synthesis. The 4G fragment can direct binding of the 40S ribosomal subunit to IRES-containing mRNAs, so viral mRNA translation is very efficient (Figure 7). These viruses also promote the dephosphorylation of BP1 (PHAS-1), thereby decreasing cap (4E)-dependent translation (see Figure 3).

Fig7. Picornaviruses disrupt the 4F complex. The 4E-4G complex (4F) directs the 40S ribosomal subunit to the typical capped mRNA (see text). However, 4G alone is sufficient for targeting the 40S subunit to the internal ribosomal entry site (IRES) of certain viral mRNAs. To gain selective advantage, some viruses (eg, poliovirus) express a protease that cleaves the 4E binding site from the amino terminal end of 4G. This truncated 4G can direct the 40S ribosomal subunit to mRNAs that have an IRES but not to those that have a cap (ie, host cell mRNAs). The widths of the arrows indicate the rate of translation initiation from the AUG codon in each example. Other viruses utilize distinct processes to effect selective initiation of translation on their cognate viral mRNAs via IRES elements.

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مواضيع ذات صلة

Posttranslational Processing Affects the Activity of many Proteins

Mutations result when changes occur in the Nucleotide Sequence

The Genetic Code is Degenerate, Unambiguous, Nonoverlapping, Without Punctuation, & Universal

RNAs can be Extensively Modified

RNA Molecules are Extensively Processed Before They Become Functional

Phosphorylation Activates Pol II

Formation of the Pol II Transcription Complex

Eukaryotic Promoters Are More Complex

Bacterial Promoters Are Relatively Simple

RNA Synthesis is A Cyclical Process that Involves RNA Chain Initiation, Elongation, & Termination

RNA is Synthesized From A DNA Template by RNA Polymerases

DNA & Chromosome Integrity Is Monitored Throughout the Cell Cycle