Shine-Dalgamo Interaction

The sequences immediately upstream from the open reading frames of both the sulfo-thermophiles and the thermophilic methanogens are presented in Table 7. Stretches of purines located 3-9 nucleotides upstream from the start codon which could interact with the polypyrimidine sequence present at the 3 terminus of each archaeal 16S rRNA (Shine Dalgamo interaction) are underlined. For the thermophilic methanogen transcripts, as for those of the methanogen and extreme halophiles [1], a purine-rich sequence, of varying length, is present at the appropriate position. However, for the sulfothermophiles... 

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... 

In the bacteria, the recognition of the initiator codon is mediated hy the interaction of the 3 end of the 16S rRNA and a purine-rich region (the Shine-Dalgamo or SD sequence) located upstream of the initiation codon [148]. Putative SD sequences have been found upstream of many archaeal r-protein genes [8,9,12,84,109,114,120,122,123,133,140,143-146,148-152]. However, in no case have these sequences been shown experimentally to interact with the 16S rRNA. In E. coli, the distance between the SD sequence and the initiation codon is critical, greater than 5 nucleotides and less than 13 [163]. Fig. 6 shows... 

These findings are interpreted to indicate that erythromycin resistance mutation in domain II caused an increase in the peptide and disrupted an indirectly functional interaction between domains II and V, because such a mutation could affect alteration of the stability of a secondary rRNA structure (hairpin sequence structure) in domain II. In addition, the Shine-Dalgamo (SD) sequence of the rRNA-encoded E-peptide ORE is sequestered in the hairpin structure. Thereby, SD and E-peptide codon are not accessible to ribosomes of wild-type E. coli. The conformational change of the hairpin structure by erythromycin resistance mutation can be recognized by ribosomes for the initiation of translation of E-peptide. Thus, the increase of the peptide is expected to show resistance to macrolide antibiotics such as erythromycin, oleandomycin, and spiramycin but not clindamycin and chloramphenicol without preventing their binding to the target. 

A purine-rich mRNA sequence, three to nine nucleotides long (called the Shine-Dalgamo sequence), which is centered about 10 nucleotides upstream of (to the 5 side of) the start codon, base-pairs with a sequence of complementary nucleotides near the 3 end of the 16S rRNA of the 30S ribosomal subunit. This interaction plus the association of fMet-tRNAf with the AUG in the P site of the ribosome sets the mRNA reading frame. 

Once associated with mRNA, the pre-initiation complex scans downstream to locate a start codon (AUG). This process is driven by ATP, and requires the helicase activity of an elF. The start codon is recognised by base paring between the anti-codon on tRNA and the AUG on the mRNA. Codon-anticodon interaction is facilitated by yet more elFs. Usually, the first AUG codon that is encountered is used, especially if it is surrounded by the so called Kozak consensus sequence (named after its discoverer Marilyn Kozak). Occasionally a later AUG is used if the first AUG not in the context of a consensus Kozak sequence, or is very close to the 5 cap. This is in contrast to prokaryotes, where the AUG that will act as a start codon is located at the future P site by the position of the ribosome after base-pairing between the 16S rRNA of the ribosome and the Shine Dalgamo sequence. 

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