Q.54 For their efficient translation, eubacterial mRNAs possess a Shine-Dalgarno sequence for its
recognition by an anti-Shine-Dalgarno sequence (ASD) in the ribosomes. The correct statement is
(A) ASD is present in 5S rRNA
(B) ASD is present in 23S rRNA
(C) ASD is present in 16S rRNA
(D) ASD is formed by the interaction of the 16S rRNA with the 23S rRNA upon docking of the
50S subunit on the 30S subunit of the ribosomes
In eubacterial translation, efficient initiation relies on the Shine-Dalgarno (SD) sequence in mRNA, which base-pairs with the anti-Shine-Dalgarno (ASD) sequence in the ribosome. This interaction positions the ribosome precisely at the start codon for protein synthesis. A common question in molecular biology exams asks: “For their efficient translation, eubacterial mRNAs possess a Shine-Dalgarno sequence for its recognition by an anti-Shine-Dalgarno sequence (ASD) in the ribosomes.” The options are:
(A) ASD is present in 5S rRNA
(B) ASD is present in 23S rRNA
(C) ASD is present in 16S rRNA
(D) ASD is formed by the interaction of the 16S rRNA with the 23S rRNA upon docking of the 50S subunit on the 30S subunit of the ribosomes
Correct Answer: (C) ASD is present in 16S rRNA
This answer stems from the structure of the bacterial 30S ribosomal subunit, where the ASD sequence—also known as the anti-Shine-Dalgarno sequence—resides at the 3′ end of the 16S rRNA. The SD sequence (typically AGGAGG or variants) in mRNA 5-10 nucleotides upstream of the AUG start codon complements this ASD region (CCUCCU), ensuring accurate 30S subunit binding during translation initiation.
Detailed Explanation of All Options
Understanding why option (C) is correct requires breaking down each choice, grounded in ribosome structure and function.
Option (A) ASD is present in 5S rRNA
Incorrect. The 5S rRNA is a component of the bacterial 50S large subunit. It plays roles in ribosome stability and peptidyl transferase activity but lacks the ASD sequence. No base-pairing with SD occurs here, as 5S rRNA is not involved in mRNA decoding.
Option (B) ASD is present in 23S rRNA
Incorrect. The 23S rRNA forms the core of the 50S subunit, housing the peptidyl transferase center for peptide bond formation. While it interacts with mRNA during elongation, it does not contain the ASD for initiation. Studies, including cryo-EM structures, confirm ASD exclusivity to 16S rRNA.
Option (C) ASD is present in 16S rRNA
Correct. Located in helix 44 at the 3′ minor domain of 16S rRNA (positions 1535-1541: 3′-AUUCCUCCACUAG-5′), the ASD directly base-pairs with the SD sequence. This was first identified by Steitz and Jakes in 1975 via footprinting assays. Mutations in this region impair translation efficiency, as shown in E. coli studies, highlighting its critical role in prokaryotic initiation—absent in eukaryotes.
Option (D) ASD is formed by the interaction of the 16S rRNA with the 23S rRNA upon docking
Incorrect. While 16S rRNA (30S) and 23S rRNA (50S) interact during 70S ribosome assembly via intersubunit bridges, the ASD pre-exists in 16S rRNA. It functions in the 30S pre-initiation complex before 50S docking. No evidence supports de novo ASD formation; this misrepresents the sequential assembly process.
Why This Matters in Biotechnology and Molecular Biology
The SD-ASD interaction is pivotal for bioengineering applications like synthetic biology and recombinant protein production in bacteria such as E. coli. Optimizing SD sequences enhances expression yields in plasmids. In research, disrupting this (e.g., via antibiotics like kasugamycin) halts translation, underscoring its therapeutic potential.
For students and researchers in microbiology or biochemistry, mastering this concept clarifies prokaryotic vs. eukaryotic translation differences—no SD in eukaryotes, which use Kozak sequences instead.
Key references include Nomura’s ribosome biogenesis work and recent structural biology from Ramakrishnan’s group (Nobel 2009).
