Initiation

eIF   Eukaryote Initiation Factors

   IF--Initiation Factors in bacteria

Eukaryotic initiation factors (eIFs) are proteins involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of the functional ribosome around the start codon and also provide regulatory mechanisms in translation initiation. Several initiation factors form a complex with the small 40S ribosomal subunit and Met-tRNAiMet called the 43S preinitation complex (PIC). Additional factors of the eIF4F complex (eIF4A, E, and G) recruit the 43S PIC to the five-prime cap structure of messenger RNA to promote ribosomal scanning along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNAiMet promotes GTP hydrolysis (or gated phosphate release) by specific initiation factors and initiation factor release, resulting in the 60S ribosomal subunit recruitment to form the 80S ribosome. There exist many more eukaryotic initiation factors than prokaryotic initiation factors, reflecting the greater biological complexity of eukaryotic cells. Eukaryotic translation requires at least twelve eukaryotic initiation factors, described below.  eIF1 to eIF6 with some subunits make up these factors.

Initiation of translation in prokaryotes involves the assembly of the components of the translation system, which are: the two ribosomal subunits (50S and 30S subunits); the mature mRNA to be translated; the tRNA charged with N-formylmethionine (the first amino acid in the nascent peptide); guanosine triphosphate (GTP) as a source of energy; the prokaryotic elongation factor EF-P and the three prokaryotic initiation factors IF1, IF2, and IF3, which help the assembly of the initiation complex. Variations in the mechanism can be anticipated.

The ribosome has three active sites: the A site, the P site, and the E site. The A site is the point of entry for the aminoacyl tRNA (except for the first aminoacyl tRNA, which enters at the P site). The P site is where the peptidyl tRNA is formed in the ribosome. And the E site which is the exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.

The selection of an initiation site (usually an AUG codon) depends on the interaction between the 30S subunit and the mRNA template. The 30S subunit binds to the mRNA template at a purine-rich region (the Shine-Dalgarno sequence) upstream of the AUG initiation codon. The Shine-Dalgarno sequence is complementary to a pyrimidine rich region on the 16S rRNA component of the 30S subunit. This sequence has been evolutionarily conserved and plays a major role in the microbial world we know today. During the formation of the initiation complex, these complementary nucleotide sequences pair to form a double stranded RNA structure that binds the mRNA to the ribosome in such a way that the initiation codon is placed at the P site.

The signals that identify initiation codons are different in prokaryotic and eukaryotic cells, consistent with the distinct functions of polycistronic and monocistronic mRNAs . Initiation codons in bacterial mRNAs are preceded by a specific sequence (called a Shine-Delgarno sequence, after its discoverers) that aligns the mRNA on the ribosome for translation by base-pairing with a complementary sequence near the 3´ terminus of 16S rRNA. This base-pairing interaction enables bacterial ribosomes to initiate translation not only at the 5´ end of an mRNA but also at the internal initiation sites of polycistronic messages. In contrast, ribosomes recognize most eukaryotic mRNAs by binding to the 7-methylguanosine cap at their 5´ terminus . The ribosomes then scan downstream of the 5´ cap until they encounter an AUG initiation codon. Sequences that surround AUGs affect the efficiency of initiation, so in many cases the first AUG in the mRNA is bypassed and translation initiates at an AUG farther downstream. However, eukaryotic mRNAs have no sequence equivalent to the Shine-Delgarno sequence of prokaryotic mRNAs. Translation of eukaryotic mRNAs is instead initiated at a site determined by scanning from the 5´ terminus, consistent with their functions as monocistronic messages that encode only single polypeptides.

<img src="/02c24fc4-a862-5d4e-ad44-af3451585092.png"/>      Initiation sites in prokaryotic mRNAs are characterized by a Shine-Delgarno sequence that precedes the AUG initiation codon. Base pairing between the Shine-Delgarno sequence and a complementary sequence near the 3´ terminus of 16S rRNA aligns the mRNA on the ribosome. In contrast, eukaryotic mRNAs are bound to the 40S ribosomal subunit by their 5´ 7-methylguanosine caps. The ribosome then scans along the mRNA until it encounters an AUG initiation codon.

Initiation

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