Organism Found in University Pond Rewrites the Rules of DNA

Scientists at the Earlham Institute and the University of Oxford have stumbled upon a discovery that alters our understanding of genetic coding. The finding emerged during tests of a novel method of single-cell DNA sequencing.

The research has been published in PLOS Genetics.

Unexpected pond finding

Dr. Jamie McGowan, a postdoctoral scientist at the Earlham Institute, made the discovery while analyzing the genome sequence of a microscopic organism called a protist. Neither animal, plant nor fungus, protists usually live in water, and the sample McGowan studied was taken from a freshwater pond at Oxford University Parks. Common protists include single-cell amoebas and algae, but also larger organisms like slime molds and kelp.

McGowan was test-running a novel DNA sequencing workflow, custom-built to analyze volumes of DNA down to the single-cell level. The analysis unexpectedly revealed that the microscopic protist was a new species, classified as Oligohymenophorea sp. PL0344.

The way that this protist converted its DNA into proteins that allow the cell to function – through processes called transcription and translation – was unlike anything else found in nature.

Stop me if you think that you’ve transcribed this gene before

Oligohymenophorea is part of a group of protists called the ciliates. They feature hair-like structures called cilia. Ciliates commonly show changes to their genetic code, including in an important genetic feature called stop codons.

During transcription, DNA code is read and converted into a complementary copy using another nucleic acid – RNA. Typically, when genes are transcribed, three stop codons – TAA, TAG and TGA – mark the termination of a gene. When changes are seen in these stop codons, TAA and TAG nearly always show the same change, which suggests that their change throughout evolution has been linked together. “In almost every other case we know of, TAA and TAG change in tandem,” said McGowan. “When they aren’t stop codons, they each specify the same amino acid.” 

But in Oligohymenophorea sp. PL0344, only TGA codes for a stop codon. The other two stop signals have been repurposed – TAA to code for the amino acid lysine and TAG for glutamic acid.

Gene revelations waiting to be discovered

“This is extremely unusual,” McGowan said. “We’re not aware of any other case where these stop codons are linked to two different amino acids. It breaks some of the rules we thought we knew about gene translation – these two codons were thought to be coupled.” 

The authors conclude that despite the last three decades of advances across genomics, there are still unexplored anomalies of the genetic code waiting to be found across nature.

“It’s sheer luck we chose this protist to test our sequencing pipeline, and it just shows what’s out there, highlighting just how little we know about the genetics of protists,” said McGowan.

Reference: McGowan J, Kilias ES, Alacid E, et al. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLOS Genetics. 2023;19(10):e1010913. doi: 10.1371/journal.pgen.1010913

This article is a rework of a press release issued by the Earlham Institute. Material has been edited for length and content.