Routine testing reveals unique genetic code variation.

Newswise – Scientists testing a new method of sequencing single cells have unexpectedly changed our understanding of the rules of genetics.

The genome of a protist has revealed a seemingly unique difference in the DNA code that marks the end of the gene, suggesting the need for further research to better understand this diverse group of organisms.

Dr Jamie McGowan, postdoctoral scientist at the Earlham Institute, analyzed the genome sequence of a microscopic organism isolated from a freshwater pond in Oxford University Park.

This work is testing a DNA sequencing pipeline to work with very small amounts of DNA, such as DNA from a single cell. Dr McGowan worked with a team of scientists at the Earlham Institute and Professor Thomas Richards’ team at the University of Oxford.

But when the researchers looked at the genetic code, the protist Oligohymenophoria sp. PL0344 turned out to be a new species, unlikely in how its DNA is translated into proteins.

Dr McGowan said: „It was pure luck that we chose this protist to test our sequencing pipeline, and it shows what’s out there, highlighting how little we know about the genetics of protists.”

It is difficult to make any statement about the protesters as a group. Most are microscopic, single-celled organisms such as amoebas, algae and diatoms, but there are large multicellular protists – such as kelp, slime molds and red algae.

„The definition of a protist is loose – basically it’s any eukaryotic organism that isn’t an animal, plant or fungus,” Dr McGowan said. „It’s apparently very common, and that’s because protists are such a diverse group.

„Some are closely related to animals, some are closely related to plants. There are predators and prey, parasites and hosts, swimmers and sessiles, and many people who have different diets when they photosynthesize. Basically, we can make very few generalizations.

Oligohymenophoria sp. PL0344 is a ciliate. These swimming protists can be seen under a microscope and are found almost anywhere there is water.

Ciliates are hotspots for genetic code changes, including rearrangement of one or more stop codons—the codons TAA, TAG, and TGA. In almost all organisms, these three stop codons are used to mark the end of a gene.

Variations in the genetic code are extremely rare. Among the few variations of the genetic code reported to date, the TAA and TAG codons almost always have the same translocation, indicating that their evolution is coupled.

„In all other cases that we know of, TAA and TAG co-evolve,” explained Dr. McGowan. „When they are not stop codons, they each specify the same amino acid.”

DNA is like a blueprint for a building. It doesn’t do anything by itself – it provides instructions for work to be done. In order to have a genetic effect, the blueprint must be „read” and then constructed into a molecule.

For DNA to be read, it is first transcribed into RNA. This copy is carried to another part of the cell, where it is translated into amino acids, which form the three-dimensional molecule. The translation process starts at a DNA start codon (ATG) and ends at a stop codon (usually TAA, TAG or TGA).

In Oligohymenophoria sp. PL0344, where TGA acts as the only stop codon – Dr McGowan found that the ciliate’s DNA contained more TGA codons than expected, but is believed to compensate for the loss of the other two. Instead, TAA refers to lysine and TAG refers to glutamic acid.

„It’s very unusual,” Dr. McGowan said. „We don’t know of any other case where these stop codons are paired with two different amino acids. This breaks some of the rules we thought we knew about gene translation—these two codons were thought to be paired.

„Scientists are trying to design new genetic codes – but they exist in nature. If we look, we can find fascinating things.

„Or, in this case, when we’re not looking for them.”

The research, published in PLoS Genetics, was funded by the Wellcome Foundation as part of the Darwin Tree of Life project, and supported by major funding from the Earlham Institute of the Biotechnology and Biological Sciences Research Council (PBSRC), part of UKRI.