Downstream RNA hairpins are found to coordinate mRNA translation

Research conducted by Duke University, Durham, discovered a position-dependent traffic jam in mRNA translation due to RNA hairpins leading to higher translation of upstream start codons (uAUGs).

In a paper, “Downstream RNA hairpins dynamically dictate initiation codon selection,” published in natureThe team describes their findings on the mechanism of translational regulation in Arabidopsis and the consequent discovery of a similar mechanism in humans. An article in News & Views in the same issue of the magazine discussed the work done by the team.

Any genome is constructed with instructions that specify when to start and stop transcribing segments of RNA. These fragments can contain multiple start codons, which can then be selectively used as starting points for the ribosome to initiate translation into proteins. The current study has identified the mechanism through which the selection process takes place between possible starting points.

Ribosomal subunits assemble onto an mRNA molecule and scan it for the start codon AUG to initiate protein synthesis. Sometimes, the first start codon encountered is used as the start, and sometimes, it is not recognized. If it is not recognized, scanning continues down the mRNA, where it may find an alternative starting point or an easily recognizable starting point (the main AUG).

The study discovered that if the mRNA contains a hairpin loop located between two start codons, the scanning process will be slowed, providing more time for recognition of the upstream start codon (uAUG), leading to a higher translation rate from this starting point.

Arabidopsis seedlings were studied under an immune response induced by the presence of elf18 (part of a bacterial protein) to determine changes in codon choice. They found that ribosomal activity at upstream start codons was decreased in response to elf18, suggesting that translation preferentially initiates at start points (primary AUGs) that are easier to recognize under these conditions.

The study identified RNA helicases, specifically RH37-like helicases, as enzymes involved in the disassembly of hairpin structures near uAUGs during the immune response in Arabidopsis. Elevated levels of these helicases under the immune response eliminated the hairpin-induced traffic jam, which then led to increased translation from the alternative start codon and thus production of a different protein.

The “if this, then that” mechanism works like a logic gate, allowing the same piece of mRNA to produce a replacement protein when the situation warrants it.

The researchers introduced a hairpin structure down the start codon of ATF4, a well-known mammalian stress-responsive gene with higher expression levels under conditions of cellular stress. This condition prevents ATF4 translation through enhanced translation initiation of a less familiar start codon.

The researchers performed an in vivo analysis on a mutant version of BRCA1 mRNA associated with breast cancer. Mutant BRCA1 mRNA is known to be regulated by the presence of multiple start codons. The analysis detected significantly lower downstream activities of uAUG2 and uAUG3 using SHAPE-MaP analysis, suggesting the presence of hairpin structures in mammalian transcripts.

Experimental results demonstrate that upstream initiation codons and hairpin structure-mediated translation initiation mechanisms are not limited to plants but also exist and function in human cells. This suggests the existence of a universal logic-gating mechanism for initiation codon selection in translation initiation across different organisms with both conserved evolutionary insights and future therapeutic targeting implications.