Initiation factors prokaryotic

Gribskov, M. (1992). Translational initiation factors IF-1 and eIF-2 alpha share an RNA-binding motif with prokaryotic ribosomal protein SI and polynucleotide phosphoryl-ase. Gene 119, 107-111. 

In this figure, the initiation factor is presented as IF. In other publications, the initiation factor is sometimes presented as eIF2 in this abbreviation, e indicates that it is an initiation factor in eukaryotic cells, since the factor in prokaryotic cells is quite distinct, and the number 2 is to indicate that, although there are many initiation factors, it is number 2 that appears to be directly involved in regulation of initiation, via a G-protein. 

The first phase of translation, initiation, involves several steps. First, two proteins, initiation factors IF-1 and IF-3, bind to the 30 S subunit (1). Another factor, IF-2, binds as a complex with GTP (2). This allows the subunit to associate with the mRNA and makes it possible for a special tRNA to bind to the start codon (3). In prokaryotes, this starter tRNA carries the substituted amino acid N-formylmethionine (fMet). In eukaryotes, it carries an unsubstituted methionine. Finally, the 50 S subunit binds to the above complex (4). During steps 3 and 4, the initiation factors are released again, and the GTP bound to IF-2 is hydrolyzed to GDP and Pj. 

In eukaryotic cells, the number of initiation factors is larger and initiation is therefore more complex than in prokaryotes. The cap at the 5 end of mRNA and the polyA tail (see p. 246) play important parts in initiation. However, the elongation and termination processes are similar in all organisms. The individual steps of bacterial translation can be inhibited by antibiotics (see p. 254). 

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... 

Initiation of protein synthesis involves the assembly of the components of the translation system before peptide bond formation occurs. These components include the two ribosomal subunits, the mRNA to be translated, the aminoacyl-tRNA specified by the first codon in the message, GTP (which provides energy for the process), and initiation factors that facilitate the assembly of this initiation complex (see Figure 31.13). [Note In prokaryotes, three initiation factors are known (IF-1, IF-2, and IF-3), whereas in eukary- otes, there are at least ten (designated elF to indicate eukaryotic origin).] There are two mechanisms by which the ribosome recognizes the nucleotide sequence that initiates translation ... 

Initiation The components of the translation system are assembled, and mRNA associates with the small ribosomal subunit. The process requires initiation factors. In prokaryotes,a purine-rich region (the Shine-Dalgarno sequence) of the mRNA base-pairs with a complementary sequence on 16S rRNA, resulting in the positioning of the mRNA so that translation can begin. The 5 -cap on eukaryotic mRNA is used to position that structure on the ribosome. The initiation codon is 5 -AUG-3. ... 

Formation of the initiation complex for protein synthesis in prokaryotes. E. coli has three initiation factors bound to a pool of 30S ribosomal subunits. One of these factors, IF-3, holds the 30S and 50S subunits apart after termination of a previous round of protein synthesis. The other two factors, IF-1 and IF-2, promote the binding of both fMet-tRNAfMel and mRNA to the 30S subunit. The binding of mRNA occurs so that its Shine-Dalgamo sequence pairs with 16S... 

Even though specific differences distinguish the initiation process in eukaryotes and prokaryotes, three things must be accomplished to initiate protein synthesis in all systems (1) The small ribosomal subunit must bind the initiator tRNA (2) the appropriate initiating codon on mRNA must be located and (3) the large ribosomal subunit must associate with the complex of the small subunit, the initiating tRNA, and mRNA. Nonribosomal proteins, known as initiation factors (IFs), participate in each of these three processes. IFs interact transiently with a ribosome during initiation and thus differ from ribosomal proteins, which remain continuously associated with the same ribosome. 

Formation of the initiation complex for protein synthesis in eukaryotes. The reaction begins with the small subunit held apart from the large subunit by an antiassociation factor and ends with the hydrolysis of GTP and joining of the large subunit as in prokaryotes. The intervening reactions are different. A much more complex spectrum of initiation factors (elFs) is involved, and the exact function of only a few of these factors is known with certainty. The... 

Initiation of protein synthesis is catalyzed by proteins called initiation factors (IFs). In prokaryotes, three initiation factors (IF1, IF2 and IF3) are essential. Because of the complexity of the process, the exact order of binding of IF1, IF2, IF3, fMet-tRNAfMet and mRNA is still unclear. One current model is shown in Fig. 4 and is described below. 

Eukaryotic ribosomes are larger (80S) and more complex than prokaryotic ribosomes (70S). Initiation is basically similar in prokaryotes and eukaryotes except that in eukaryotes at least nine initiation factors are involved (cf. three factors in prokaryotes), the initiating amino acid is methionine (cf. N-formylmethionine in prokaryotes), eukaryotic mRNAs do not contain Shine-Dalgarno sequences (so the AUG initiation codon is detected by the ribosome scanning instead), and eukaryotic mRNA is monocistronic (cf. some polycistronic mRNAs in prokaryotes). Initiation in eukaryotes involves the formation of a 48S preinitiation complex between the 40S ribosomal subunit, mRNA, initiation factors and Met-tRNA 61. The ribosome then scans the mRNA to locate the AUG initiation codon. The 60S ribosomal subunit now binds to form the 80S initation complex. 

Elongation in eukaryotes requires three eukaryotic initiation factors that have similar functions to the corresponding prokaryotic proteins. 

Initiation of protein synthesis in eukaryotes requires at least nine distinct eukaryotic initiation factors (elFs) (see Table 1) compared to the three initiation factors (IFs) in prokaryotes (see Topic H2). 

Both prokaryotes and eukaryotes initiate protein synthesis with a specialized methionyl-tRNA in response to an AUG initiation codon. Eukaryotes, however, use an initiator met—tRNAmeti—that is not formylated. Recognition of the initiator AUG is also different. Only one coding sequence exists per eukaryotic mRNA, and eukaryotic mRNAs are capped. Initiation, therefore, uses a specialized capbinding initiation factor to position the mRNA on the small riboso-mal subunit. Usually, the first AUG after the cap (that is, 3 to it) is used for initiation. 

Translation in prokaryotes begins with the formation of the ribosome complex at a defined position on the mRNA, termed the Shine-Delgamo sequence, or the ribosome binding site (RBS). In prokaryotic mRNA, this is a relatively small (4-7 nucleotides) region rich in purine nucleotides located less than 10 nucleotides to the 5 side of the translational start site (Fig. 23-3). This Shine-Delgarno sequence is complementary to the 16S ribosomal RNA (rRNA) associated with the 30S ribosomal subunit, and directs it to bind the mRNA at that position. The 3 OS ribosomal subunit will not bind this region on the mRNA without the aid of an associated protein called initiation factor 3 (IF-3). The 30S ribosomal subunit will bind the mRNA in such a manner that the peptidyl (P) site of the complex is occupied by a specialized codon with the sequence, AUG. It is at this AUG start codon where translation will eventually begin. 

Eukaryotic translation initiation is far more complicated than the prokaryotic system described earlier. To begin the process, two initiation factor... 

Figure 29.27. Translation Initiation in Prokaryotes. Initiation factors aid the assembly first of the 308 initiation complex and then of the 70S initiation complex.

Protein synthesis takes place in three phases initiation, elongation, and termination. In prokaryotes, mRNA, formylmethionyl-tRNAf (the special initiator tRNA that recognizes AUG), and a 308 ribosomal suhunit come together with the assistance of initiation factors to form a 308 initiation complex. A 508 rihosomal suhunit then joins this complex to form a 708 initiation complex, in which fMet-tRNAf occupies the P site of the rihosome. 

Eukaryotes utilize many more initiation factors than do prokaryotes, and their interplay is much more intricate. The prefix elF denotes a eukaryotic initiation factor. For example, eIF-4E is a protein that binds directly to the 7-inethylguanosine cap (p. 846), whereas eIF-2, in association with GTP, delivers the met-tRNA to the ribosome. The difference in initiation mechanism between prokaryotes and eukaryotes is, in part, a conseciuence of the ence in RNA processing. The 5 end of mRNA is readily available to ribosomes immediately after transcription in prokaryotes. In contrast, pre-mRNA must be processed and transported to the cytoplasm in eukaryotes before translation is initialed. The 5 cap provides an easily recognizable starting point. In addition, the complexity of eukaryotic translation initiation provides another mechan ism for regulation of gene expression that we shall explore further in Chapter 31. 

A list of key differences between prokaryotes and eukaryotes with respect to protein synthesis is shown in Table 9-1. These include the existence of multiple eukaryotic initiation factors that facilitate the assembly of the riboso-mal protein synthetic machinery, whereas there are only three for prokaryotes. An initiation site on bacterial mRNA consists of the AUG initiation codon preceded with a gap of approximately 10 bases by the Shine-Dalgamo polypurine hexamer, whereas the 5 Cap (a 7-methylguanylate residue in a 5 —>5 triphosphate linkage) acts as an initiation signal in eukaryotes. In prokaryotes, the first or A-terminal amino acid is a formyl-methionine (fMet), but in eukaryotes it is usually a simple methionine. Additionally, the size and nature of the prokaryotic ribosomes are quite different from the eukaryotic ribosomes. 

Eukaryotes use a more complex spectrum of initiation factors than prokaryotes. There are at least nine eukaryotic initiating factors (elFs), several of which possess numerous subunits. The functional roles of most of these factors are still under investigation. 

The major differences between prokaryotic and eukaryotic translation control mechanisms are related to the complexity of eukaryotic gene expression. Features that distinguish eukaryotic translation include mRNA export (spatial separation of transcription and translation), mRNA stability (the half-lives of mRNA can be modulated), negative translational control (the translation of certain mRNAs can be blocked by the binding of specific repressor proteins), initiation factor phosphorylation (mRNA translation rates are altered by certain circumstances when eIF-2 is phosphorylated), and translational frame-shifting (certain mRNAs can be frame-shifted so that a different polypeptide is synthesized). 

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