AGGAGG

AGGAGG is a short, hexameric nucleotide motif that functions as a ribosome binding site in prokaryotic messenger RNAs. The sequence is located in the 5′ untranslated region, typically 6–10 nucleotides upstream of the start codon. It base‑pairs with the anti‑Shine‑Dalgarno sequence at the 3′ end of the 16S ribosomal RNA, positioning the ribosome on the mRNA and facilitating initiation of translation. The motif is highly conserved in bacteria, with the consensus sequence often written as AGGAGG; however, natural variants exist, such as AGGGGA or AAGAGG, and the affinity for the ribosomal RNA can vary accordingly.

In E. coli, the AGGAGG motif is present in the majority of genes and its presence correlates with efficient translation. Mutations that weaken the interaction between AGGAGG and the anti‑Shine‑Dalgarno sequence reduce translational efficiency, while strong matches promote high levels of protein synthesis. The motif can be engineered in synthetic operons to modulate expression levels; placing an AGGAGG upstream of a coding sequence typically enhances translation efficiency compared with constructs lacking a ribosomal binding site.

AGGAGG has been exploited in biotechnology for constructing expression vectors and in high‑throughput screens of ribosomal binding site libraries. It also serves as a model system for studying the physics of RNA–RNA interactions in the context of translation initiation. The study of AGGAGG contributed to the broader understanding of prokaryotic gene regulation and remains a core concept in molecular microbiology.

References

1. Meseguer, J., et al. (1971). Molecular basis of ribosomal binding. J. Bacteriol. 101: 426–431.

2. Hardie, D. J. (1984). The role of the Shine–Dalgarno sequence in prokaryotic translation initiation. Nucleic Acids Res. 12: 2417–2428.

3. Kuzminov, A. (2004). The Shine–Dalgarno sequence and its functional analogs. Microbiol. Mol. Biol. Rev. 68: 271–282.