Researchers at the University of California, Berkeley have discovered that a microorganism known as Methanosarcina acetivorans can interpret its genetic code with ambiguity, challenging a fundamental principle in biology. Typically, each three-letter codon in DNA corresponds to a single amino acid or signals the end of protein synthesis. However, this archaeal microbe sometimes interprets the UAG codon both as a stop signal and as an instruction to add the rare amino acid pyrrolysine, resulting in two different proteins.
“Objectively, ambiguity in the genetic code should be deleterious; you end up generating a random pool of proteins,” said Dipti Nayak, assistant professor of molecular and cell biology at UC Berkeley and senior author of the study published on November 6 in Proceedings of the National Academy of Sciences. “But biological systems are more ambiguous than we give them credit to be and that ambiguity is actually a feature — it’s not a bug.”
The research indicates that this flexibility may help Methanosarcina acetivorans digest methylamine—a compound found commonly in environments such as the human gut—by incorporating pyrrolysine into necessary enzymes. This finding has potential implications for human health because certain archaea and bacteria play roles in metabolizing compounds linked to cardiovascular disease.
Introducing controlled imprecision into how cells read genetic codes could also offer new ways to treat diseases caused by premature stop codons, which prevent proper protein formation. These conditions account for about 10% of all genetic diseases, including cystic fibrosis and Duchenne muscular dystrophy.
In most organisms studied so far, codons are either assigned to one amino acid or serve as stop signals. Some exceptions exist where organisms use additional amino acids like pyrrolysine by reinterpreting specific codons but still maintain one meaning per codon. The discovery that Methanosarcina acetivorans can randomly choose between stopping or adding an amino acid at UAG is unique.
“It’s essentially like a cipher,” Nayak explained. “You’re taking something in one language and translating it into another, nucleotides to amino acids.”
Nayak noted that many archaea produce pyrrolysine: “Now that you have a new amino acid, the world’s your oyster,” she said. “You can start playing around with the much larger code. It’s like adding one more letter to the alphabet.”
Katie Shalvarjian, now at Lawrence Livermore National Laboratory and co-author on the paper, added: “We found that the machinery required to create pyrrolysine is widespread in the Archaea, especially amongst these methanogenic archaea that consume methylated amines.” She observed during her research that UAG was not always interpreted consistently: “The UAG codon is like a fork in the road, where it can be interpreted either as a stop codon or as a pyrrolysine residue,” Shalvarjian said. “We think whether or not a protein exists primarily in its elongated or in its truncated form might form a regulatory cue for the cell.”
Despite efforts to find cues guiding this decision-making process within cells’ sequences or structures, none were identified. Nayak commented: “The methanogens have not recoded UAG, nor have they added any new factors to make it deterministic… They just do both and they seem to be fine by making this random choice.”
Preliminary data suggest that cellular levels of pyrrolysine influence whether UAG is read as an addition point for this amino acid or as a stop signal; higher concentrations bias toward incorporation into proteins.
“This really opens the door to finding interesting ways to control how cells interpret stop codons,” Nayak said.
Funding for this work came from several sources including Searle Scholars Program and Chan-Zuckerberg Biohub-San Francisco investigator support.
