AUG, codon

Figure 38-10. Picornavimses disrupt the 4F complex. The 4E-4G complex (4F) directs the 40S ribosomal subunit to the typical capped mRNA (see text). 4G alone is sufficient for targeting the 40S subunit to the internal ribosomal entry site (IRES) of viral mRNAs. To gain selective advantage, certain viruses (eg, poliovirus) have 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. The widths of the arrows indicate the rate of translation initiation from the AUG codon in each example.

Kwon H-S, Lee D-K, Edenberg HJ, Lee J-J, Ahn Y-H, Hur M-W. Post-transcriptional regulation of human ADH5/FDH and Myf6 gene expression by upstream AUG codons. Arch Biochem Biophys 2001 386 163-171. 

A gene encodes a protein with 150 amino adds. There is one intron of 1000 bps, a 5 -untranslated region of 100 bp and a 3 -nntranslated re on of 200 bp. In the final processed mRNA, how many bases lie between the start AUG codon and the final termination codon ... 

The mRNA of eucaryotes does not possess specific initiation sequences. Rather, the AUG start codon is identified by scanning the eucaryotic mRNA the 408 subunit of the ribosome threads the 5 non-translated end of the mRNA and uses the first AUG codon encoimtered to initiate translation. Whether a AUG codon is used as an initiator depends, additionally, upon the sequence context. If the sequence environment is unfavorable for initiation, then the scanning is continued and initiation occurs at one of the next AUG. With the help of this leaky scanning" strategy it is possible to produce proteins with different N-termini from the same mRNA. 8ince there are often signal sequences foimd at the N-terminus, this mechanism may lead to alternative com-partmentalization of a protein. 

The fimction of eIF-2 is illustrated schematically in Fig. 1.55. eIF-2 belongs to the superfamily of regulatory GTPases (see ch. 5). elF-2 fulfills the task of bringing the methionyl-initiator-tRNA to the 40S subimit of the ribosome. The active eIF-2 GTP form binds the methionyl-initiator-tRNA, associates with the cap structure of the mRNA, then commences to scan along the mRNA. Once an AUG codon is encoimte-red, the boimd GTP is hydrolyzed to GDP, resulting in the dissociation of the... 

How can the single (5 )AUG codon distinguish between the starting At-formylmethionine (or methionine, in eukaryotes) and interior Met residues The details of the initiation process provide the answer. 

Explain how the protein synthesizing machinery is able to differentiate the initiation AUG codon from an internal AUG (methionine) codon in prokaryotes. How is this accomplished in eukaryotes ... 

Model for attenuation in the trp operon, showing ribosome and leader RNA. (a) Where no translation occurs, as when the leader AUG codon is replaced by an AUA codon, stem-and-loop 3.4 is intact, and termination in the leader is favored. (b) Cells are selectively starved for tryptophan so that the ribosome stops prematurely at the tandem trp codons. Under these conditions, stem-and-loop 2.3 can form, and this is believed to lead to the disruption of stem-and-loop 3.4. (c) All amino acids, including excess tryptophan, are present so that stem-and-loop 3.4 is present. 

The process of translation can be divided into three stages initiation, elongation, and termination. Usually, the AUG codon next to the mRNA cap is used to initiate translation. It is thought that a 43 S preinitiation... 

Transcription occurs in the 5 to the 3 direction for the mRNA. The AUG codon would start peptide synthesis and Gly would be the C-terminal amino acid. Peptide synthesis would continue until a stop codon (in this case, UAA) appears. The peptide fragment from the DNA strand would be ... 

Chejanovsky, N. and Carter, B. J. (1989). Mutagenesis of an AUG codon in the adeno-associated virus rep gene Effects on viral DNA replication. Virology 173, 120-128. 

The first codon translated in all mRNAs is AUG which codes for methionine. This AUG is called the start codon or initiation codon. Naturally, other AUG codons also occur internally in an mRNA where they encode methionine residues internal to the protein. Two different tRNAs are used for these two types of AUG codon tRNAfMet is used for the initiation codon and is called the initiator tRNA whereas tRNAmMet is used for internal AUG codons. In prokaryotes the first amino acid of a new protein is /V-formylmethionine (abbreviated fMet). Hence the aminoacyl-tRNA used in initiation is fMet-tRNAfMet. It is essential that the correct AUG is used as the initiation codon since this sets the correct reading frame for translation (see Topic HI). A short sequence rich in purines (5 -AGGAGGU-3 ), called the Shine-Dalgarno sequence, lies 5 to the AUG initiation codon (Fig. 3) and is complementary to part of the 16S rRNA in the small ribo-somal subunit. Therefore this is the binding site for the 30S ribosomal subunit... 

The context of the mRNA sequence around the AUG codon translational start site, where the ribosome initiates translation of protein synthesis, is an important consideration. An appropriate consensus ribosome-binding region for the host organism should be used and potentially inhibitory RNA secondary structure, that may affect the ability of the ribosome to access this translation start site, avoided. Various RNA structure prediction programs such as... 

Toward the 5 end of mRNA, there is a region of 20 or so nucleotides before the initiation codon AUG is reached. This leader region contains a sequence responsible for interaction of the mRNA with the 30S subunit. It is known as the Shine-Dalgarno (S-D) sequence, and it can bind to a complementary sequence at the 3 end of the 16S rRNA to position the 30S subunit appropriately for initiation. Other sequences in the leader region are possibly involved in the overall process of initiation of translation, which involves also the binding of the appropriately charged methionyi-tRNA opposite the AUG codon. 

Why can t tRNAm1 1 function in initiation of polypeptide synthesis from an appropriate AUG codon ... 

The consequence of sequence changes at the DNA level on the sequence of encoded protein is shown by the example in Table 2.3, where an AUG codon representing methionine in proteins is subjected to single base changes. The various types of mutations and their influence on information transfer are illustrated in Box 2.1. 

Formylation of methionylated tRNA " allows differentiation of the AUG start codon from internal AUG codons (14). MetRS aminoacylates tRNA" with methionine. A formyl group is linked covalently to the charged methionine via its amino moiety by the methionyl-tRNA formyltransferase enzyme, which uses N -formyl tetrahydrofolate as the formyl donor. This fMet-tRNA molecule binds directly to the P site of the ribosome to initiate protein synthesis, as compared with the A-site to which elongator tRNAs bind. 

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