Question

Nonsense-mediated decay is an mRNA surveillance pathway that eliminates mRNAs with premature stop codons. How does the cell distinguish between normal mRNAs and those with a premature stop?

Short answer

Question: Explain how the nonsense-mediated mRNA decay (NMD) pathway distinguishes between normal mRNAs and those with a premature stop codon, and how it eliminates faulty mRNAs. Answer: The NMD pathway distinguishes between normal mRNAs and those with a premature stop codon by checking for the presence of an Exon Junction Complex (EJC) near the stop codon. In normal mRNAs, the stop codon is located after the last exon junction, and all EJCs are displaced by ribosomes during translation. In contrast, premature stop codons are located before the last EJC, which leads to close proximity between the ribosome, EJC, and stop codon. This proximity recruits additional factors, such as Upf1, Upf2, and Upf3, to form the NMD complex, which interacts with release factors and triggers rapid degradation of the faulty mRNA.

Step-by-step solution

Introduction to Nonsense-mediated mRNA Decay (NMD)

NMD is a quality control mechanism in cells that identifies and degrades mRNAs containing premature stop codons, thereby preventing the production of truncated, potentially harmful proteins.

Understanding normal mRNA translation

During translation, ribosomes read mRNA sequences and synthesize the corresponding proteins. The mRNA has start (AUG) and stop (UAA, UAG, or UGA) codons that signal the beginning and end of translation, respectively.

Exon Junction Complex and its role in mRNA surveillance

During mRNA splicing, an Exon Junction Complex (EJC) is deposited on the mRNA 20-24 nucleotides upstream of every exon-exon junction. EJCs serve as markers that are displaced by ribosomes during the first round of translation called pioneer translation.

Scanning for premature stop codons

When the ribosome encounters a stop codon during translation, specific proteins named release factors (RF) come into play. In the case of a premature stop codon, the ribosome and the EJC will be in close proximity due to the presence of the stop codon before the EJC has been displaced.

Activation of NMD pathway

The close proximity of the ribosome and EJC during the translation of premature stop codons recruits additional factors, such as Upf1, Upf2, and Upf3, to form the NMD complex. This complex interacts with the release factors and triggers the rapid degradation of the mRNA containing premature stop codon.

Mechanism for distinguishing normal mRNAs

In normal mRNAs, the stop codon is located after the last exon junction. During translation, ribosomes displace all EJCs, and therefore, no EJCs are present near the correct stop codon when translation ends. In the absence of EJCs, the NMD factors are not recruited, and normal mRNAs are not targeted for degradation. In summary, the nonsense-mediated mRNA decay pathway distinguishes between normal mRNAs and those with a premature stop codon by the presence of an Exon Junction Complex near the stop codon, which leads to the formation of the NMD complex and subsequent degradation of the faulty mRNA.