Shine-Dalgamo sequence

The small ribosomal subunit binds to the mRNA. In prokaryotes, the 16S rRNA of the small subunit binds to the Shine-Dalgamo sequence in the 5 untranslated region of the niRNA. In eukaryotes, the small subunit binds to the 5 cap structure and slides down the message to the first AUG. 

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. 

Complementary binding between prokaryotic mRNA Shine-Dalgamo sequence and 16S rRNA. 

One of the most prominent features of the 50S subunit is the LI protuberance, seen on the left side in Fig. 29-6A. This protuberance is formed almost entirely by protein LI, which is one of the largest ribosomal proteins. It binds to the 2105-2184 loop in domain V of the 23S RNA (see Fig. 29-14).139 LI has an important regulatory role in bacteria in which it represses translation of its own structural gene by binding to a region in its mRNA close to the Shine-Dalgamo sequence. 

Most eukaryotic mRNAs have a 5 cap (p. 1642) and lack a Shine-Dalgamo sequence. Otherwise, initiation follows a pattern similar to that in bacteria but more complex.305-308 There are at least ten eukaryotic... 

Shine-Dalgamo sequence Signal recognition particle proteasome... 

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... 

Fig. 1. Vector for protein expression in the periplasmic space of E. coli. Expression is controlled by an IPTG inducable lac promotor. SD is the Shine-Dalgamo sequence, OmpA is the signal sequence of the outer membrane protein A of E. coli followed by the RANTES cDNA.

By selectively changing sequences in E. coli translation initiation region with randomized calliper inputs and observing the corresponding neural network performance, Nair (1997) analyzed the importance of the initiation codon and the Shine-Dalgamo sequence. 

In the crenarchaeota (exemplified by only Sulfolobus), Shine-Dalgamo sequences are not an obligatory feature. Certain Sulfolobus genes (notably the EF-la [33], EF-2 [34] and RNA polymerase rpoC genes [18]) exhibit potential Shine-Dalgamo motifs located immediately upstream of the initiator ATG, whereas others (notably, the ribosomal... 

Alignment of putative Shine-Dalgamo sequences of sulfothermophiles and thermophilic... 

Recognition sequence Shine-Dalgamo sequence 5 caps direct e-IEs... 

Describe how the base pairing between the Shine-Dalgamo sequence and the 30S subunit provides a mechanism for distinguishing a start codon from a methionine codon. What is the eukaryotic version of this mechanism ... 

Prokaryotes - Prokaryotic mRNAs are synthesized on the bacterial nucleoid in direct contact with the cytosol and are immediately available for translation. The Shine-Dalgamo sequence (see here) near the 5 end of the mRNA binds to a site on the prokaryotic ribosomal RNA (rRNA), allowing attachment of the ribosome and initiation of translation, often even before transcription is completed. 

Eukaryotes - In eukaryotes, the mRNA is produced in the nucleus and must be exported into the cytosol for translation. Furthermore, the initial product of transcription (pre-mRNA) may include introns, which must be removed before translation can occur. There is no ribosomal attachment sequence like the Shine - Dalgamo sequence in prokaryotes. For all these reasons, eukaryotic mRNA requires extensive processing before it can be used as a protein template. This processing takes place while mRNA is still in the nucleus. 

Just before the AUG start codon, prokaryotic mRNAs have a common sequence called the Shine-Dalgamo sequence. Some variations on the sequence are shown in Table 27,3. The Shine-Dalgamo sequences are complementary to a sequence contained in the 16S ribosomal RNA (rRNA) (Table 27.3) and help align the mRNA with the ribosome to properly orient the molecules for translation initiation. 

Near the 3 end of the 16S rRNA is a sequence (3 - UCCUCC -5 ) that can base pair with a sequence near the 5 end of each mRNA. The sequence in the mRNA is called the Shine-Dalgamo sequence (see here). This pairing aligns the message correctly for the start of translation. 

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