Shine-Dalgarno sequence, translation initiation

The Shine-Salgano interaction is a base pairing interaction that occurs during translation initiation in prokaryotes between the Shine-Dalgarno sequence on messenger RNA (mRNA) and the anti-Shine-Dalgamo... 

Translation Initiation 305 subrmit binds to Shine-Dalgarno sequence on mRNA j 40S subunit assodates with 5 cap on mRNA... 

As opposed to the case in procaryotes, eucaryotic translation does not require a specific sequence for the binding of the ribosome. Procaryotes rely on the Shine-Dalgarno sequence, which is complementary to sequences of the 16S RNA of the 308 subunit. The Shine-Dalgamo sequence mediates the binding of mRNA to the 308 ribosome and ensures the correct positioning of the AUG initiation codon. 

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. ... 

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 ribosome has a problem similar to that of RNA polymerase the ribosome must find the point in the mRNA at which to begin translation. In prokaryotes the site is marked by a tract called the Shine-Dalgarno sequence, about ten nucleotides upstream from the initiation site. Initiation occurs at the first subsequent AUG sequence. (AUG codes for the amino acid methionine.) In eukaryotes, initiation usually begins simply at the first AUG sequence from the 5 -end of the mRNA. 

Formation of the translational initiation complex in bacteria involves ribosome interactions with a sequence in the mRNA that is upstream (50) of the AUG and called the Shine-Dalgarno sequence. The purine-rich Shine-Dalgarno sequence (AGGAGG) is complementary to a portion of the 16S rRNA. Step 1 involves the interaction of IF-1 and IF-3 with the 30S ribosome subunit to form a complex which is positioned precisely at the initiator codon (AUG). The addition of IF-2, GTP, and the f-Met-tRNAf-Met result in the formation of the preinitiation complex in step 2. In step 3, hydrolysis of GTP and the release of IF-2 and IF-1 allows for the binding of the 50S ribosome subunit which completes the assembly of the initiation complex. The P and A sites are also schematically... 

Shine-Dalgarno sequence Binding site for the SOS ribosome on an mRNA for translation initiation, terminator Signal for RNA polymerase to stop transcription and release the DNA template and the nascent transcript. 

When the ribosomal subunits separate, the 30S subunit may not always dissociate from its mRNA. For example, in polycistronic messages (more than one protein coded on an mRNA), the 30S subunit may simply slide along the mRNA until the next Shine-Dalgarno sequence (see here) and initiation codon are encountered and begin a new round of translation. 

How does the ribosome know where to start translating In prokaryotic translation, the correct AUG start codon is identified by its proximity to a consensus sequence called the Shine-Dalgarno sequence. This sequence is complementary to a sequence on the small subunit of the prokaryotic ribosome. The ribosome is initially positioned on the Shine-Dalgarno sequence, which aligns it for correct translation initiation at the start codon. 

No. This is in marked contrast to the situation in bacterial mRNA that may contain multiple Shine-Dalgarno sequences that permit binding by ribosomes to initiate translation from multiple start sites. In eukaryotes, the mRNA that codes for protein is monocistronic and hence codes for a single protein. One explanation for why this comes about is that each eukaryotic mRNA molecule has only a single 5 cap that recruits ribosomes, and thus translation cannot be initiated from multiple start sites on the same mRNA molecule, although alternative start sites may be used. 

During the processing of primary transcripts that are destined for mRNA formation in eukaryotes, a methylated guanine cap is attached to the 5 end. This is essential for efficient initiation of translation of the mature eukaryotic mRNA, and it does not occur in prokaryotes. In prokaryotes, rRNA in the small ribosomal subunit binds first to the Shine-Dalgarno sequence of the mRNA, before binding tRNA. In eukaryotes, the ribosome binds first to the 5 cap and then scans along the mRNA, using the tRNA to detect the AUG codon. 

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. 

By contrast, eucaryal mRNAs are translated after extensive modifications of the primary transcripts that yield mature (generally capped and polyadenylated) monocistronic mRNAs. Recognition of translation start sites does not rely upon Shine-Dalgarno recognition instead, the small ribosomal subunit (generally) binds to the capped 5 end of mRNA and scans its nucleotide sequence until the initiator AUG codon is encountered. The polypeptide chains are initiated by a non-formylated methionine and the initiation reactions are aided by as many as 8-10 protein factors, some of which possess ATPase activity and perform functions not encountered in bacteria, such as cap recognition and mRNA unwinding (for a detailed review see ref [4]). 

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