The Shine-Dalgarno sequence (or Shine-Dalgarno box), proposed by Australian scientists John Shine (b.1946) and Lynn Dalgarno (b.1935), is a ribosomal binding site in the mRNA, generally located 8 bases upstream of the start codon AUG. The Shine-Dalgarno sequence exists both in bacteria and archaea, being also present in some chloroplastic and mitochondial transcripts. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGU. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (UCCUCC), is called the anti-Shine-Dalgarno sequence and is located at the 3' end of the 16S rRNA in the ribosome. The eukaryotic equivalent of the Shine-Dalgarno sequence is called the Kozak sequence.
Mutations in the Shine-Dalgarno sequence can reduce or increasetranslation. This change is due to a reduced or increased mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the anti-Shine-Dalgarno sequence can restore translation.
The Shine-Dalgarno sequence GAGG dominates in bacteriophage T4 early genes, whereas the sequence GGAG is a target for the T4 endonuclease RegB that initiates the early mRNA degradation.
When the Shine-Dalgarno sequence and anti-Shine-Dalgarno sequence pair, the translation initiation factors IF2-GTP, IF1, IF3, as well as the initiator tRNA fMet-tRNA(fmet) are recruited to the ribosome.
The ribosomal S1 protein in Gram-negative bacteria
In Gram-negative bacteria, the presence of a Shine-Dalgarno sequence is not obligatory for the ribosome to locate the initiator codon. Numerous prokaryotic mRNAs don't possess Shine-Dalgarno sequences at all: ribosomal protein S1, which binds to AU-rich sequences found in many prokaryotic mRNAs 15-30 nucleotides upstream of start-codon, can instigate translation initiation in the case of these mRNAs.
SD-Sequences in Chloroplasts
Although plastids are prokaryotic descendants and still have their prokaryotic translational machinery, SD-like sequences are not required at least in green alga Chlamydomonas reinhardtii chloroplasts according to a study.
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