Messenger RNA: Interaction with Ribosomes

Anne Carr-Schmid, UMDNJ Robert Wood Johnson Medical School, Piscataway, New Jersey, USA Terri Goss Kinzy, UMDNJ Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
The recruitment and binding of a messenger RNA (mRNA) to the ribosome is a highly specific and regulated process. This process depends on unique sequences and structures within the mRNA, soluble auxiliary factors as well as the RNA and protein components of the ribosome to allow the synthesis of proteins.

Introductory article
Article Contents
. Introduction . The ShineDalgarno Sequence . 30S SubunitmRNA Interaction . Role of Initiation Factors . 5 CapRibosome Interactions . Scanning Mechanisms and the Kozak Consensus . Internal Ribosome Entry Sites . mRNA Interactions with rRNA and with Ribosomal Proteins . Movement of mRNA during Translocation

Introduction
Translation is the step of converting triplets of nucleotide sequence of a messenger RNA (mRNA) template into the corresponding amino acid sequence of a protein. The process of translating an mRNA into a protein is dependent upon the formation of a complex between the mRNA and the ribosome (Figure 1). Ribosomes, which consist of one-third protein and two-thirds RNA, contain both a large and a small subunit. The small ribosomal subunit, with the aid of associated soluble protein initiation factors, initially attaches at or near the 5 end of the mRNA coding region. Prokaryotic, eukaryotic and viral mRNA must all interact with ribosomes in order to be translated. However, key dierences exist in the mechanisms by which these various mRNAs initially associate with ribosomes. Positioning of the small subunit over the translation initiation start site of the mRNA, or start codon, permits the base-pairing interaction between this codon and the anticodon of the initiator tRNA. Formation

of the initiation complex signals the binding of the large ribosomal subunit and dissociation of associated factors. The complete ribosome proceeds along the mRNA, moving three nucleotides at a time, to provide the next codon of the mRNA. The next aminoacyl transfer RNA (aa-tRNA) can then bind and donate its amino acid to the elongating polypeptide chain. Elongation factors facilitate both the binding of an aa-tRNA and the movement of the mRNA through the ribosome. Additionally, tRNAs help to maintain the contact between the ribosome and the mRNA. This process continues until the polypeptide chain is complete and the ribosome dissociates. The initial interaction between the small subunit of the ribosome and the mRNA determines which mRNAs are used as templates for translation. The ribosome also serves to provide the coordinating site for the recognition event that occurs between all codons of an mRNA and the anticodons of aa-tRNAs, Thus, interactions between the mRNA and the ribosome are critical for the selection of the translation start site and the continued accurate decoding of the mRNA template.

50S 5 tRNA AA 3 mRNA 30S

The ShineDalgarno Sequence

In prokaryotes, the small ribosomal subunit (the 30S subunit) recognizes an mRNA molecule as a template for translation by binding directly to specic sequences called ribosome-binding sites (RBSs). RBSs were originally identied in the 1970s as regions of mRNA protected by the ribosome from degradation by ribonucleases. Sequence analysis of the RBSs of numerous mRNA templates indicated the presence of two sequence-specic elements. The rst element of the RBS is the translation start site signal, or start codon. In prokaryotes, the start codon is typically AUG although GUG and UUG codons are also utilized. The second element in the RBS is a short, purinerich sequence, termed the ShineDalgarno (SD) sequence (Figure 2a).
1

50

Figure 1 The prokaryotic 70S ribosome is composed of a small (30S) and a large (50S) subunit. The 30S ribosomal subunit binds first and defines the start codon of the open reading frame, followed by joining of the 50S subunit. The complete ribosome continually moves down the messenger RNA (mRNA), adding amino acids and translocating the messenger RNA across the ribosomal RNA platform of the 30S subunit, three bases at a time. AA, amino acid; tRNA, transfer RNA.

ENCYCLOPEDIA OF LIFE SCIENCES 2001, John Wiley & Sons, Ltd. www.els.net

Messenger RNA: Interaction with Ribosomes

U A A G G A G G U X (a)

A U G

m7G (b)

G C C R C C

A U G

Figure 2 General features of the 5 untranslated regions (5-UTRs) of prokaryotic and eukaryotic mRNAs. (a) The prokaryotic ShineDalgarno consensus sequence (italics) is upstream of the AUG. (b) The eukaryotic mRNA contains a 5 7-methylguanosine (m7G) cap and the Kozak consensus sequence element surrounding the AUG.

Since prokaryotic mRNAs are polycistronic, that is, they code for two or more polypeptides (Figure 3), the SD serves to dierentiate an AUG codon that functions as a translation start site signal from an AUG within the coding region of an mRNA. The start site of the rst proteincoding region is typically preceded by a short 5 untranslated region (5-UTR), while subsequent AUGs can be directly at or even upstream of the stop codon of the preceding protein-coding region. The SD is typically located approximately seven nucleotides before the start codon. The role of the SD sequence was demonstrated by the ability of point mutations in the SD of an mRNA to inhibit its translation. The mechanism by which the SD sequence functions to facilitate the translation of an mRNA became evident upon sequence analysis of the 16S ribosomal RNA (rRNA) of the small subunit. The SD sequence was complementary to a highly conserved sequence present within the 3 end region of the 16S rRNA sequence (5-ACCUCCUUA-3). The complementarity between the SD region of the mRNA and the 16S rRNA suggested the potential for base-pairing interactions between the two sequences. Base-pairing interactions were conrmed by enzymatic digestion of initiation complexes on mRNA templates. Regions of base pairing were resistant to digestion and, depending upon the mRNA template used, involved 39 nucleotides. A biological role for the base-pairing reaction was conrmed when the translation defect of an mRNA with a mutated SD was suppressed by the expression of ribosomes with compensatory mutations introduced into their 16S rRNA.
SD

Therefore, the SD serves to anchor the small ribosomal subunit to the mRNA through base-pairing interactions with the 16S rRNA component of the small subunit. The RBS region of an mRNA clearly plays an important role in the initiation of translation. Consequently, control of an RBS is an important way the cell can regulate the translation of a specic mRNA. RNA-binding proteins termed repressors can bind directly to the RBS region of an mRNA and prevent 30S ribosome binding. Alternatively, repressor proteins have been identied that bind to specic regions within an mRNA to stabilize RNA structures that prevent the bound 30S ribosome from forming a functional initiation complex. A classic example of this second mechanism of regulation involves ribosomal protein S4 (rpS4). When too much rpS4 protein has been synthesized, the extra rpS4 protein will bind to its own mRNA. rpS4 functions as a repressor protein by stabilizing a conformation of the rpS4 mRNA in which the start codon is not accessible for base pairing with the anticodon of the initiator tRNA. When rpS4 protein is bound to the rpS4 mRNA, its translation is decreased until the levels of rpS4 protein decrease within the cell.

30S SubunitmRNA Interaction

The small ribosomal subunit functions as the coordinating site for the interactions between the codon of the mRNA and anticodon of the tRNA during translation. Consequently, the small subunit must provide binding sites for both mRNA and tRNA, in the absence of the 50S subunit. A large portion of the 3 end of the 16S rRNA is an RNA platform which runs along the interface of the 30S subunit where the 50S subunit binds. Crosslinking studies indicate that upon mRNA binding there are several contacts between the mRNA and the 3 end of the 16S rRNA, including the ShineDalgarno interaction. The ribosome contains two aa-tRNA-binding sites, the acceptor site (A site) and the peptidyl site (P site). The initiator tRNA enters directly into the P site of the small ribosomal subunit, while all other aa-tRNAs initially enter the ribosomal A site. The crystal structure of the ribosome shows that rRNA components of the 30S subunit P site anchor both the codon on the mRNA and the anticodon of the tRNA in the P site.

AUG UAA
Start Stop

SD

AUG

SD

AUGA UAA

Role of Initiation Factors

The formation of the 30S initiation complex necessitates a recognition event between the start codon of an mRNA and the anticodon of an initiator tRNA on the small ribosomal subunit. In prokaryotes, three initiation factors (IFs) have been identied that accelerate the formation of translation initiation complexes. The three factors, IF1,

Figure 3 Prokaryotic mRNAs are polycistronic, containing multiple open reading frames (ORFs, boxes) where each initiation codon is downstream of the ShineDalgarno sequence (SD) and the region between the ORFs can vary; it may even overlap with the termination codon of the prior ORF.

Messenger RNA: Interaction with Ribosomes

IF2 and IF3, are found to associate with the 30S subunit and are released from the small subunit upon 70S ribosome formation. The IFs function to maintain a pool of free 30S subunits to initiate translation. They also monitor the basepairing interaction that occurs between the start codon of the mRNA and the anticodon of the initiator tRNA. Consequently, the IFs inuence both the rate and specicity of 30S subunit/mRNA/initiatortRNA complex formation. The cell contains a uctuating pool of nontranslating ribosomes. In prokaryotes, this pool constitutes approximately 20% of all ribosomes. The ribosomes may exist as 70S couples (30S and a 50S bound together) or as free 30S and 50S subunits. Only ribosomes that have dissociated into subunits can be used in the process of translation initiation. One of the functions attributed to the IFs is the maintenance of a free pool of 30S subunits for translation initiation. IF1 functions as a dissociation factor and transiently associates with 70S couples to promote their dissociation into free subunits. In contrast, IF3 functions as an antiassociation factor by binding free 30S subunits and preventing their reassociation with free 50S subunits. The IFs do not inuence the base-pairing reaction between the SD region of the mRNA and the 3 end of the 16S rRNA. Instead they inuence the base-pairing reaction between the start codon of the mRNA and the anticodon of the initiator tRNA. A 30S subunit complexed with IF1, IF2 and IF3 has the ability to bind both mRNA and initiator tRNA. The isolation of 30S complexes bound to either mRNA or initiator tRNA indicates there is no specic order in which the mRNA and initiator tRNA interact with the complex. When the 30S complex binds the SD region of the mRNA, IF2 and its cofactor guanosine triphosphate (GTP) function to bind and position the initiator tRNA into the P site of the 30S subunit. IF1 and IF3, in addition to their function described above, stabilize the binding of the initiator tRNA on the 30S at a start codon. IF3 also destabilizes both initiation complexes that form at nonstart codons and initiation complexes that form with aa-tRNAs other than the initiator tRNA. The ability of IF3 to eectively monitor the codonanticodon interaction on the 30S subunit is consistent with the determination that the IF3-binding site on the 30S is in close proximity to the binding site for the anticodon of the P site tRNA. A correct base-pairing interaction between the mRNA and tRNA at the start codon results in the release of IF3. Consequently, the 50S subunit-binding site is no longer blocked on the 30S. The 50S subunit joins the initiation complex and stimulates GTP hydrolysis by IF2. GTP hydrolysis results in the dissociation of both IF1 and IF2 from the 70S complex, signalling the end of the initiation phase of translation.

5 CapRibosome Interactions
Unlike prokaryotes, sequence-specic base-pairing interactions between the mRNA and rRNA have not been identied for the selection of eukaryotic mRNAs as templates for translation. Instead, eukaryotic mRNA must interact with a complex set of initiation factors before the small (40S) subunit of the ribosome can bind to the mRNA. Translation of most eukaryotic mRNAs is strongly dependent upon the presence of a 7-methylguanosine (m7G) cap at the 5 end of the mRNA molecule (Figure 2b). The cap structure serves as a nucleation site for a translation initiation factor (eIF) complex called eIF4F. The eIF4F complex consists of multiple proteins involved in cap binding, RNA unwinding and forming a bridge between initiation factors and the 40S subunit. In addition to bringing the small subunit into close proximity of the mRNA to allow the 40S/mRNA complex to form, the eIF4A subunit of the eIF4F complex also functions to unwind the mRNA downstream of the cap structure, ensuring single-stranded regions are available for ribosome binding. This process requires energy in the form of adenosine triphosphate (ATP) as demonstrated by the fact that depletion of ATP blocks the ribosomal subunit at or near the cap. The 40S subunit binds eIF3 (a multisubunit translation initiation factor) and the ternary complex of eIF2GTP initiator-tRNA to form a 43S complex. This complex interacts with the eIF4F complex, bound to the mRNA. Thus, unlike prokaryotes, the initiator tRNA is always bound by the small ribosomal subunit before interaction with the mRNA. Consistent with the importance of the formation of the cap-binding complex on the mRNA, circularization of an mRNA prevents the 43S complex from binding. Alteration of the activities of the components of the eIF4F complex has been identied as a key regulatory mechanism for inhibiting protein synthesis, by preventing the recruitment of the 43S complex to mRNA.

Scanning Mechanisms and the Kozak Consensus

In prokaryotes, the small ribosomal subunit binds directly to the translation start site to initiate translation. However, in eukaryotes, once the 40S subunit attaches upstream of the coding region of the mRNA, it migrates or scans down the mRNA until it reaches the translation start site. For eukaryotic mRNAs, the translation start site is typically the rst AUG codon in the mRNA. Natural mRNAs are not linear and signicant secondary structure can exist within the 5-UTR. The ability of the 40S subunit/initiator-tRNA/initiation factor complex to position itself at the rst AUG codon requires the ribosome
3

Messenger RNA: Interaction with Ribosomes

to penetrate secondary structures present within the 5UTR. The introduction of stemloop structures between the m7G cap and the rst AUG of the mRNA can inhibit scanning of the ribosome complex. The degree of inhibition correlates with the strength and positioning of the secondary structure. Secondary structure directly adjacent to the m7G cap drastically inhibits translation by preventing the small ribosomal subunit from binding the mRNA. The ability of secondary structure further downstream of the cap structure to inhibit the scanning of the ribosome depends upon the stability of the secondary structure. The RNA-unwinding activity required for ribosomal scanning is attributed to the eIF4A subunit of the eIF4F complex. The 40S subunit/initiator-tRNA/initiation factor complex scans the mRNA until it recognizes an AUG codon. Initial and correct positioning of the complex at the AUG codon requires the activity of additional factors. Alteration in the activity of several initiation factors can prevent the formation of initiation complexes over the authentic start codon. For example, genetic evidence demonstrates the important role of eIF2 and the initiator tRNA anticodon in the recognition of the start codon at the P site. For eukaryotic mRNAs, the rst AUG is preferentially used. The residues that ank the rst AUG codon of an mRNA can aect the eciency with which the rst AUG codon is recognized by the scanning 40S subunit/initiatortRNA/initiation factor complex. Comparison of the translation initiation start sites of vertebrate mRNAs indicate a bias toward the presence of a specic consensus sequence, GCCRCCaugG, termed the Kozak consensus, named for Dr. Marilyn Kozak who initially identied the consensus sequence. The most highly conserved position in the consensus sequence is the 2 3 position (3 residues before the A of the AUG). Mutation of the 2 3 position purine residue, which is usually an A, dramatically reduces translation initiation. A change in the G residue at the 1 4 position (the rst residue directly following the AUG) also aects the eciency of initiation. The role of the other residues of the Kozak consensus is not as signicant when the 2 3 and 1 4 positions are conserved. Consequently, an AUG codon is identied as being surrounded by a weak or strong context depending upon the residues present at the 2 3 and 1 4 positions. The mechanism by which codon context aects the translation initiation process has not been demonstrated. One possibility is that interaction between the 40S ribosomal subunit complex and the Kozak consensus might serve to slow scanning during migration along the mRNA, thus enhancing the recognition of the start codon. Similarly, the presence of small amounts of secondary structure downstream of an AUG start codon can function to enhance start codon recognition. The secondary structure may also function to slow down the scanning 40S subunit complex. In fact, the reduced recognition of an AUG codon in a weak context can be suppressed by the

introduction of secondary structure downstream of the AUG codon.

Internal Ribosome Entry Sites

Specic viral mRNA molecules are capable of engaging the cellular protein synthesis machinery, despite lacking many of the features that are associated with eciently translated cellular mRNA molecules. Also, despite rapid inhibition of the host cell protein synthesis upon viral infection, translation of these viral mRNA molecules remains uninhibited. An alternative cap-independent mechanism of translation initiation, termed internal initiation, is known to occur on these viral mRNAs. Internal initiation is dependent on the presence of a unique element termed an internal ribosome entry site (IRES) in the 5-UTR of the viral mRNA (Figure 4). IRES elements have been identied in Hepatitis C virus, certain retroviruses and in several cellular mRNAs. However, the structure of IRES elements and factors involved in their function have been most thoroughly studied for members of the Picornaviridae family. Picornaviral infection results in rapid inhibition of host cell functions, including protein synthesis. One mechanism by which several of the picornaviruses, such as poliovirus, interfere with cap-dependent translation of cellular mRNAs is through inhibition of the activity of the eIF4F complex, consequently inhibiting binding of the small

A B

(a)

IRES A

AUG

(b)

IRES

AUG

Figure 4 The general classes of viral internal ribosome entry sites (IRESs) in the 5 untranslated region of the messenger RNA contain significant secondary structure, conserved stemloops A and B, and polypyrimidine tracks (black boxes). They deposit the 40S subunit at (a) or near (b) the AUG.

Messenger RNA: Interaction with Ribosomes

ribosomal subunit complex to the mRNA. Despite viralinduced inhibition of cellular protein synthesis, the uncapped picornavirus mRNAs continue to be eciently translated. Picornavirus mRNAs possess long 5-UTRs, ranging from 650 to 1300 nucleotides, that contain multiple AUG codons and regions of signicant secondary structure. Identication of single point mutations within the 5-UTR of attenuated (noninfectious) poliovirus isolates suggested a role for the 5-UTR regions in replication of the virus in neuronal cells, potentially through facilitating translation of the viral mRNA. In fact, insertion of the 5-UTR region of the poliovirus mRNA midpoint between two open reading frames (ORFs) present in a bicistronic construct directs ecient translation of the second ORF, independent of translation of the upstream ORF. Subsequent deletion studies have dened the minimal region of the viral mRNA 5-UTR element sucient for directing internal initiation of translation, referred to as an IRES. For most picornavirus family members, the IRES elements are approximately 450 nucleotides long. The ability of a picornavirus IRES to direct initiation within a circular RNA, which lacks a free RNA terminus, further conrms that initiation occurs by an internal mechanism. Two main classes of IRES elements have been dened based on their common predicted secondary structures and on their location within the 5-UTR relative to the AUG codon utilized in the initiation of translation. There is little overall similarity between the two major types of IRES structures (Figure 4). However, all IRES elements are characterized by two conserved stemloop structures, A and B, and a polypyrimidine tract. IRES elements located directly adjacent to the translation start site likely recruit the small ribosomal subunit directly to the authentic AUG, thus functioning in a manner similar to the prokaryotic ribosome-binding site (Figure 4a). However, a second class of IRES elements exist that are not directly adjacent to the translation start site (Figure 4b). Instead, they are present further upstream of the translation start site. Increasing the distance between the second class of IRES elements and the authentic AUG codon does not aect the ability of the IRES to direct internal initiation at that codon. However, introduction of additional AUG codons upstream of the authentic AUG codon does markedly reduce the initiation from the authentic AUG. These observations support the model that IRESs of the second class are dependent upon ribosomal scanning after initial binding of the ribosome complex to the viral mRNA. The exact mechanism by which the IRES recruits the small ribosomal subunit to the viral mRNA is not known. Furthermore, viral-encoded proteins are not essential for picornavirus IRES function. However, dierences in the ability of IRES elements to function in various cell types suggest that cell-specic factors may be required. The exact mechanism by which these proteins may serve to facilitate IRES-mediated internal initiation remains unclear.

Cellular mRNAs have been identied that appear to contain IRES elements. Translation of mammalian BiP (GRP78) mRNA in picornavirus-infected cells led to its identication as the rst cellular mRNA containing an IRES. Several other potential IRES containing mRNAs have been identied in mammals, fruities and Bakers yeast. Further investigation into a role for cellular IRES utilization and the cellular factors involved in the process is ongoing.

mRNA Interactions with rRNA and with Ribosomal Proteins

As mentioned above, the SD interaction with the 16S rRNA is important for the ribosomemRNA interaction in translation initiation. Furthermore, the 16S rRNA platform region of the 30S subunit is also involved in 30S subunit interactions with the mRNA. Despite the presence of 21 dierent ribosomal proteins in the prokaryotic 30S subunit, limited information exists for specic roles of ribosomal proteins in mRNA binding. Prokaryotic ribosomal protein S1 (rpS1) is an example of a ribosomal protein for which evidence of a specic role in mRNA binding has been demonstrated. rpS1 is essential for the binding of the 30S subunit to the mRNA. It is believed to function in maintaining the mRNA in a single-stranded state to facilitate ribosome binding. rpS1 has been demonstrated to bind RNA and to function to unwind RNA structure. It contains an RNAbinding region, which has high binding anity for pyrimidine rich sequences. Interestingly, analysis of many prokaryotic mRNAs indicates that pyrimidine-rich sequences commonly occur upstream of the SD sequence. mRNAs that contain an RBS at their very 5 end do not require rpS1 for translation. The lack of requirement for this essential factor is thought to arise from the lack of secondary and tertiary structure surrounding the RBS.

Movement of mRNA during Translocation

Once selection of the translation start site initially occurs, the reading frame for that particular polypeptide is determined. Consequently, through each step of aa-tRNA binding, peptide bond formation, and translocation of the tRNA and mRNA along the ribosome, the movement of the mRNA must occur three nucleotides at a time for the reading frame to be maintained. However, the movement of mRNA through the ribosome requires that contacts break and reform. How is the translation reading frame maintained? The codonanticodon interaction between the tRNA and the mRNA, which occurs on the small
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Messenger RNA: Interaction with Ribosomes

ribosomal subunit, is critical for linking the ribosome and the mRNA. The 3 ends of the A site and P site tRNA (where the amino acids or peptide chain are bound) interact with the large subunit. In order to move the mRNA and base-paired tRNA relative to the ribosome and maintain the translation reading frame, interactions must always be maintained with at least one ribosomal subunit. Peptide bond formation is accompanied by a shift in the interaction of the A site and P site tRNAs with the large subunit. The interactions of these tRNAs with the small subunit and mRNA, however, remain intact. This results in the dierent ends of the tRNAs occupying dierent tRNA-binding sites on the small and large subunits, termed the hybrid state. In the hybrid state, the anticodon region of the A site tRNA remains bound at the A site of the small subunit, while the region of the A site tRNA that interacts with large subunit moves to bind the P site region of the large subunit. Likewise, the anticodon region of the P site tRNA remains bound to the P site of the small subunit, while the other end of the tRNA now associates with the exit site (E site) of the large subunit. Translocation involves the movement of the ends of the tRNA bound to mRNA at the small subunit. The process of translocation requires both energy and a special

elongation factor. Each tRNA moves relative to the small ribosomal subunit, while remaining bound to the large subunit. The codonanticodon interaction of the mRNA and tRNA facilitates the movement of the mRNA positions a new codon at the A site and maintains the translational reading frame. Thus, as in many cases above, soluble protein factors and the tRNAs help to bind and position the mRNA on the ribosome.

Further Reading
Belsham GJ and Sonenberg N (1996) RNAprotein interactions in regulation of picornavirus RNA translation. Microbiology Reviews 60: 499511. Cate JH, Yusupov MM, Yusupova GZ, Earnest TN and Noller HF (1999) X-ray crystal structures of 70S ribosome functional complexes. Science 285: 20952104. Garrett RA, Douthwaite SR, Liljas A et al. (2000) The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. Washington, DC: ASM Press. Hershey JWB, Sonenberg N and Mathews MB (2000) Translation Control of Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Kozak M (1999) Initiation of translation in prokaryotes and eukaryotes. Gene 234: 187208.