SD Sequence - The Binding Site of Ribosomes and mRNA

What Is the SD Sequence

The SD sequence (Shine-Dalgarno sequence) was first proposed by scientists John Shine and Lynn Dalgarno in 1974. The SD sequence is the binding site of ribosomes on mRNA, usually located 6-8 bases upstream of the start codon AUG in the non-coding region. The length of the SD sequence is about 4-6 nucleotides and usually consists of A/G bases. The SD sequence combines with 16S ribosomal RNA (rRNA), and the ribosome located on this sequence can recognize and initiate the translation process, thus converting mRNA to protein. The SD sequence generally exists in prokaryotes and has also been found in ancient bacteria, chloroplasts, and mitochondria. It is worth mentioning that the SD sequence is not an essential component of all bacterial genes, and some bacterial promoters do not contain the SD sequence.

Function of SD Sequence

The SD sequence helps recruit ribosomes to mRNA, aligning them with the start codon to initiate protein synthesis. The complementary sequence is known as the anti-SD sequence, located at the 3' end of the ribosome's 16S rRNA. When the SD sequence and anti-SD sequence complementarily bind, translation initiation factors IF1, IF2, IF3, and fMet-tRNA are recruited to the small subunit of the ribosome, promoting the formation of the translation initiation complex. Different SD sequences have varying degrees of impact on mRNA translation efficiency and speed. In addition, the sequence between the SD sequence and the start codon AUG also has a significant impact on translation initiation efficiency. Experimental results show that if the base following the SD sequence is AAAA or UUUU, translation efficiency is highest, while if it is CCCC or GGGG, translation efficiency decreases to 50% and 25%, respectively. In addition to playing an important role in bacterial translation, similar sequences have also been discovered in other biological systems. This indicates that the SD sequence plays an important role in the evolution of life and is crucial for cell survival and reproduction. Therefore, in addition to conducting in-depth research on the SD sequence in bacteria, exploration of similar sequences in other biological systems is necessary to uncover more mysteries of life.

Fig. 1 The possible dual impacts of Shine-Dalgarno (SD) sequences on protein synthesis.¹

The function of the SD sequence is similar to that of the well-known 5' cap in mammalian cells, as it serves as an important auxiliary element for bacterial translation and plays a crucial role in gene expression in bacteria. Further research on the SD sequence and its recognition mechanism for promoters will help us better understand the fundamental principles of protein synthesis. Creative Biolabs has assembled an experienced and professional team dedicated to ribosome research, providing a wide range of ribosome research related technical services to global customers.

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Reference

1. Yang, Chuyue, et al. "Depletion of Shine-Dalgarno sequences within bacterial coding regions is expression dependent." G3: Genes, Genomes, Genetics 6.11 (2016): 3467-3474.