Prokaryotic elongation factors

Elongation factors Eukaryotic elongation factors (eEFs) Prokaryotic elongation factors (EFs)... 

Upon being formed by the aaRSs, aa-tRNAs are trapped by the elongation factor EF-Tu in prokaryotes and EF-IA in eukaryotes and archaea and carried to the ribosome where they are used for elongation of the... 

Abbreviations aa-tRNA Amino-acyl tRNA eLF Eukaryotic translation initiation factor IF Prokaryotic translation initiation factor eEF Eukaryotic translation elongation factor EF Prokaryotic translation elongation factor eRF Eukaryotic translation termination factor (release factor) RF Prokaryotic translation release factor RRF Ribosome recycling factor Rps Protein of the prokaryotic small ribosomal subunit Rpl Protein of the eukaryotic large ribosomal subunit S Protein of the prokaryotic small ribosomal subunit L Protein of the prokaryotic large ribosomal subunit PTC Peptidyl transferase center RNC Ribosome-nascent chain-mRNA complex ram Ribosomal ambiguity mutation RAC Ribosome-associated complex NMD Nonsense-mediated mRNA decay... 

Ribosome recycling factor (RRF) and elongation factor-G (EF-G) are required to recycle the prokaryotic ribosome back to a new round of initiation after termination (Nakamura and Ito 2003). No recycling factor has been identified so far in the cytoplasm of eukaryotic cells. To explain this difference it has been postulated that eukaryotic eRF3 has a dual function ... 

The elongation cycle in eukaryotes is quite similar to that in prokaryotes. Three eukaryotic elongation factors (eEFla, eEFljSy, and eEF2) have functions analogous to those of the bacterial elongation factors (EF-Tu, EF-Ts, and EF-G, respectively). Eukaryotic ribosomes do not have an E site uncharged tRNAs are expelled directly from the P site. 

At the conclusion of the initiation process, the ribosome is poised to translate the reading frame associated with the initiator codon. The translation of the contiguous codons in mRNA is accomplished by the sequential repetition of three reactions with each amino acid. These three reactions of elongation are similar in both prokaryotic and eukaryotic systems two of them require nonribosomal proteins known as elongation factors (EF). Interestingly, the actual formation of the peptide bond does not require a factor and is the only reaction of protein synthesis catalyzed by the ribosome itself. 

The elongation stage of translation in eukaryotes requires three elongation factors, eEFla, eEFI[3y and eEF2, which have similar functions to their prokaryotic counterparts EF-Tu, EF-Ts and EF-G (see Table 1). 

Another example of protective protein expression is the tetracycline resistance TetO and TetM proteins and their analogues (87). These proteins structurally resemble the prokaryotic GT-Pase elongation factors such as EF-G and EF-Tu that bind to the ribosome and are essential for translation. TetO/M protection proteins do not replace elongation factors, but they do bind to the ribosome and displace bound tetracyclines in a GTP-dependent manner (88, 89). 

Elongation and termination. Eukaryotic elongation factors EFla and EFip y are the counterparts of prokaryotic EF-Tu and EF-Ts. The GTP form of EFla delivers aminoacyl-tRNA to the A site of the ribosome, and EFip y catalyzes the exchange of GTP for bound GDP. Eukaryotic EF2 mediates GTP-driven translocation in much the same way as does prokaryotic EF-G. Termination in eukaryotes is carried out by a single release factor, eRFl, compared with two in prokaryotes. Finally, eIF3, like its prokaryotic counterpart IF3, prevents the reassociation of ribosomal subunits in the absence of an initiation complex. 

Figure 3-25. The initiation (A) and elongation (B) reactions of protein synthesis. EF-1 and EF-2 are eukaryotic elongation factors corresponding to EF-Tu and EF-G in prokaryotes.

C. mRNA supplies the codons, aminoacyl-tRNA and GTP provide energy, peptidyl transferase catalyzes the formation of peptide bonds, and elongation factor 2 translocates the peptidyl-tRNA. Formylmethionyl-tRNA is involved in initiation of protein synthesis in prokaryotes. 

Elongation ami Termination. Eukaryotic elongation factors KF1 a and EFl (By are the counterparts of prokaryotic EF-Pu and EF-Ts. The GTP form of EFl tv delivers aminoacyl-tRNA to the A site of the ribosome, and EFl catalyzes the exchange of GTP for bound GDP. 

Studies using intact ricin and its individual A and B chains with intact 80 S ribosomes and their 60 S and 40 S subunits have firmly established that the A chain is the toxic moiety and that it inhibits protein synthesis by inactivating a function of the 60S ribosomal subunit [113,114]. Prokaryotic 70S ribosomes, on the other hand, are insensitive to the toxin [115]. The A chain inactivates 60 S subunits catalytically [13, 15] and as a result elongation factor 2 (EF-2) is unable to bind to the subunit and protein synthesis does not occur. 

Prokaryotic initiation factors. In addition to the ribosomal proteins, the initiation factors IFl, IF2, and IF3, whose molecular masses are 9.5, 9.7, and 19.7 kDa, respectively, " are essential. They coordinate a sequence of reactions that begins with the dissociation of 70S ribosomes into their 30S and 50S subunits. Then, as is shown in Fig. 29-10, the mRNA, the initiator tRNA charged with formylmethionine, the three initiation factors, and the ribosomal subunits react to form 70S programmed ribosomes, which carry the bound mRNA and are ready to initiate protein synthesis. IF2 is a specialized G protein (Chapter 11), which binds and hydrolyzes GTP. It resembles the better known elongation factor EF-Tu (Section 2). The 172-residue IF3 consists of two compact a/p domains linked by a flexible sequence, which may exist as an a Its C-terminal domain binds to the central domain of the 16S RNA near nucleotides 819-859 (Fig. 

Fig. 15.10. Elongation of a pol5 peptide chain. 1. Binding of valyl-tRNA to the A site. 2. Formation of a peptide bond. 3. Translocation. After step 3, step 1 is repeated using the aminoacyl-tRNA for the new codon in the A site. Steps 2 and 3 follow. These three steps keep repeating until termination occurs. (In prokaryotes, an exit site called the E site binds the t-RNA after it is displaced from the P site). EE = elongation factor.

The process of elongation is very similar in prokaryotes, except that the corresponding factor for EFla is named EF-Tu and the associating elongation factors are called EF-Ts instead of EFipy. 

Translocation in eukaryotes involves another G protein, elongation factor EF2 (EF-G in prokaryotes) that complexes with GTP and binds to the ribosome, causing a conformational change that moves the mRNA and its base-paired tRNAs with respect to the ribosome. The uncharged tRNA moves from the P site and is released from the ribosome. The peptidyl-tRNA moves into the P site, and the next codon of the mRNA occupies the A site. During translocation, GTP is hydrolyzed to GDP, which is released from the ribosome along with the elongation factor (see Fig. 15.10). 

Peptide chain elongation in eukaryotes is very similar to that of prokaryotes. The same mechanism of peptidyl transferase and ribosome translocation is seen. The structure of the eukaryotic ribosome is different in that there is no E site, only the A and P sites. There are two eukaryotic elongation factors, eEFl and eEF2. The eEFl consists of two subunits, eEFlA and eEFlB. The 1A subunit is the counterpart of EF-Tu in prokaryotes. The IB subunit is the equivalent of the EF-Ts in prokaryotes. The eEF2 protein is the counterpart of the prokaryotic EF-G, which causes translocation. 

Many of the differences between translation in prokaryotes and eukaryotes can be seen in the response to inhibitors of protein synthesis and to toxins. The antibiotic chloramphenicol (a trade name is Ghloromycetin) binds to the A site and inhibits peptidyl transferase activity in prokaryotes, but not in eukaryotes. This property has made chloramphenicol useful in treating bacterial infections. In eukaryotes, diphtheria toxin is a protein that interferes with protein synthesis by decreasing the activity of the eukaryotic elongation factor eEF2. 

Eukaryotic peptide elongation follows similar processes as prokaryotes via aminoacyl-tRNA binding, transpeptidation and translocation, involving the A, P and E sites of the ribosome. Two elongation factors, EFl and EF2 mediate the elongation steps. EFl consists of two components, EFl A equivalent of EF-Tu and EFIB equivalent of EF-Ts. EF2 is the translocation factor that binds GTP and catalyzes hydrolysis of GTP that accompanies translocation. 

Ihinslational factors. Included among the GTPases involved in protein biosynthesis (see) are the initiation factors IF-2 (prokaryotes) and eIF-2 (eukaryotes) and the elongation factors EF-TU EF-G (prokaryotes) and eEF-TU (or EF-la) eEF-G (or EF-2) (eukaryotes). 

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