Rosa Rubicondior: Creationism Refuted - A Common Protist In An Oxford Pond Refutes Common Design

The end of genes: routine test reveals unique divergence in genetic code | Earlham Institute

When working as a Senior Medical Research Technician for Oxford University, one of my pleasures on a sunny Summer day was to take a lunch break walking in the University Parks with colleagues, where we could watch first class cricket free, or, more interestingly, explore the ponds and banks of the Cherwell. Little did we know that almost 60 years later, an organism living in one of those ponds would yield up such compelling evidence that life is the result of an evolutionary process, with no evidence of divine intervention.

Creationists often cite the near-universality of the genetic code as evidence of a single designer using the same system for all life. Of course, the more obvious scientific explanation is common ancestry: all living organisms inherited the same basic translation system from a remote common ancestor, with later lineages modifying it in small but revealing ways. But even on creationist terms, the argument is a hostage to fortune, because if the same code supposedly points to the same designer, then differences in that code raise the obvious question: why would the same designer do the job in different ways?

That awkward question is neatly illustrated by research from the Earlham Institute, published in PLOS Genetics. The research concerns a single-celled ciliate, Oligohymenophorea sp. PL0344, found in a pond in Oxford University Parks, which has done something highly unusual with its genetic code. Codons that normally act as full stops in genes have been reassigned so that, instead of telling the cell to stop making a protein, they now code for amino acids.

This is not a trivial detail. The genetic code is the rulebook by which DNA and RNA sequences are translated into proteins. In most organisms, three particular codons act as stop signals, marking the end of a gene’s protein-coding sequence. Altering those signals might be expected to cause chaos, yet here is an organism in which evolution has tinkered with one of biology’s most fundamental systems and produced a viable alternative arrangement.

For creationists, this creates a familiar problem. The genetic code is invoked when it appears convenient to claim common design, but its exceptions are quietly ignored because they point instead to historical contingency, descent with modification, and evolutionary experimentation. Biology is not showing us the work of an omniscient engineer standardising a perfect system; it is showing us inherited systems being modified, repurposed and patched by evolution.

What Is the Genetic Code? The genetic code is the set of rules by which living cells translate genetic information into proteins. DNA stores information in sequences of four chemical “letters” — A, C, G and T. When a gene is used, its DNA sequence is copied into messenger RNA, where T is replaced by U. The cell then reads this RNA sequence three letters at a time.

Each three-letter unit is called a codon. Most codons specify one of the amino acids used to build proteins. For example, a particular codon might instruct the cell to add lysine, leucine or glutamic acid to a growing protein chain. In this way, the order of codons in a gene determines the order of amino acids in the protein.

There are 64 possible codons, but only about 20 standard amino acids, so the code is redundant: several different codons can specify the same amino acid. This redundancy can reduce the effect of some mutations, because a change in one DNA letter does not always alter the amino acid that is inserted.

Three codons normally act as stop signals. Instead of coding for an amino acid, they tell the cell that the protein is complete and that translation should end. These stop codons are essential punctuation marks in the genetic instructions.

The genetic code is often described as nearly universal because the same basic codon assignments are shared across bacteria, archaea, plants, fungi, animals and many other organisms. This near-universality is powerful evidence that all life inherited the code from a common ancestor. However, “nearly” is the important word. Some organisms, especially certain single-celled eukaryotes and mitochondria, use modified versions of the code in which particular codons have been reassigned.

These exceptions are not failures of evolutionary theory; they are exactly the sort of historical tinkering evolution predicts. They show that even one of life’s most fundamental systems is not fixed by design, but can change over time when natural selection and cellular mechanisms allow it.

The work of the team led by Dr Jamie McGowan of the Earlham Institute is described in their press release:

The end of genes: routine test reveals unique divergence in genetic code
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 divergence in the DNA code signalling the end of a gene, suggesting the need for further research to better understand this group of diverse organisms.

Dr Jamie McGowan, a postdoctoral scientist at the Earlham Institute, analysed the genome sequence of a microscopic organism - a protist – isolated from a freshwater pond at Oxford University Parks.

The work was intended to test a DNA sequencing pipeline to work with very small amounts of DNA, such as DNA from a single cell. Dr McGowan was working with a team of scientists at the Earlham Institute and with Professor Thomas Richards’ group at the University of Oxford.

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

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.

Dr Jamie McGowan, lead author
Earlham Institute
Norwich, UK.

It is hard to make any statements about protists as a group. Most are microscopic, single-celled organisms like amoebas, algae, and diatoms, but larger multicellular protists exist – such as kelp, slime moulds, and red algae.

The definition of a protist is loose - essentially it is any eukaryotic organism which is not an animal, plant, or fungus. This is obviously very general, and that’s because protists are an extremely variable group. Some are more closely related to animals, some more closely related to plants. There are hunters and prey, parasites and hosts, swimmers and sitters, and there are those with varied diets while others photosynthesise. Basically, we can make very few generalisations.

Dr Jamie McGowan.

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

In Oligohymenophorea sp. PL0344, only TGA functions as a stop codon.

Ciliates are hotspots for genetic code changes, including reassignment of one or more stop codons - the codons TAA, TAG, and TGA. In virtually all organisms, these three stop codons are used to signal the end of a gene.

Variations in the genetic code are extremely rare. Among the few variants of the genetic code reported to date, the codons TAA and TAG virtually always have the same translation, suggesting that their evolution is coupled.

In almost every other case we know of, TAA and TAG change in tandem,” explained Dr McGowan. “When they aren’t stop codons, they each specify the same amino acid.

Dr Jamie McGowan.

DNA is like a blueprint of a building. It does not do anything in and of itself – it provides instructions for work to be done. In order for a gene to have an impact, the blueprint must be “read” and then built into a molecule which has a physical effect.

For DNA to be read, it is first transcribed into an RNA copy. This copy is taken to another area of the cell where it is translated into amino acids, which are combined to make a three-dimensional molecule. The translation process starts at the DNA start codon (ATG) and finishes at a stop codon (normally TAA, TAG, or TGA).

In Oligohymenophorea sp. PL0344, only TGA functions as a stop codon - although Dr McGowan found there are more TGA codons than expected in the ciliate’s DNA, believed to compensate for the loss of the other two. Instead, TAA specifies lysine and TAG specifies glutamic acid.

This is extremely unusual. 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. Scientists attempt to engineer new genetic codes - but they are also out there in nature. There are fascinating things we can find, if we look for them.

Or, in this case, when we are not looking for them.

Dr Jamie McGowan.

Publications:
McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, et al. (2023)
Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids.
PLoS Genet 19(10): e1010913. https://doi.org/10.1371/journal.pgen.1010913

McGowan J, Richards TA, Hall N, Swarbreck D (2024)
Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates. PLoS Genet 20(12): e1011512. https://doi.org/10.1371/journal.pgen.1011512

Abstract
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the “universal” genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3’UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.

Author summary
The genetic code is almost universal across life. The vast majority of organisms use the canonical genetic code, which has three stop codons (UAA, UAG, and UGA) and 61 sense codons that code for amino acids. Here, we report the discovery of an unexpected genetic code variant in an uncultured ciliate species from the Oligohymenophorea class, where the canonical stop codons UAA and UAG have been reassigned to code for lysine and glutamic acid, respectively. This is a particularly unusual genetic code reassignment as UAA and UAG differ at the wobble position and their evolution is thought to be coupled. We also report that the remaining stop codon, UGA, is enriched immediately downstream of genes in the same reading frame, suggesting a possible role in minimising deleterious consequences in the event of translational readthrough. Our work documents, for the first time, a genetic code variant where the codons UAA and UAG specify two different amino acids and shows that there are still unexplored genetic code reassignments awaiting discovery.

McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, et al. (2023)
Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids.
PLoS Genet 19(10): e1010913. https://doi.org/10.1371/journal.pgen.1010913

Copyright: © 2023 The authors.
Published by PLoS. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Abstract The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the ’ciliates’) are the most prominent exception to this norm, exhibiting the greatest diversity of nuclear genetic code variants and evidence of repeated changes in the code. In this study, we report the discovery of multiple independent genetic code changes within the Phyllopharyngea class of ciliates. By mining publicly available ciliate genome datasets, we discovered that three ciliate species from the TARA Oceans eukaryotic metagenome dataset use the UAG codon to putatively encode leucine. We identified novel suppressor tRNA genes in two of these genomes which are predicted to decode the reassigned UAG codon to leucine. Phylogenomics analysis revealed that these three uncultivated taxa form a monophyletic lineage within the Phyllopharyngea class. Expanding our analysis by reassembling published phyllopharyngean genome datasets led to the discovery that the UAG codon had also been reassigned to putatively code for glutamine in Hartmannula sinica and Trochilia petrani. Phylogenomics analysis suggests that this occurred via two independent genetic code change events. These data demonstrate that the reassigned UAG codons have widespread usage as sense codons within the phyllopharyngean ciliates. Furthermore, we show that the function of UAA is firmly fixed as the preferred stop codon. These findings shed light on the evolvability of the genetic code in understudied microbial eukaryotes.

Author summary
The genetic code dictates the translation of nucleotide sequences into amino acids. It is one of the most conserved features of molecular biology. Most organisms use the “standard genetic code”, where 61 codons encode amino acids and three stop codons (UAA, UAG, and UGA) signal translation termination. Ciliates–microbial single-celled eukaryotes–are the most prominent exception, with multiple lineages exhibiting variant genetic codes in which one or more stop codons have been reassigned to function as sense codons. In this study, we report novel genetic code changes in poorly studied ciliates. By analysing marine metagenomic data from the TARA Oceans Project, we identified an uncultivated lineage of ciliates from the Phyllopharyngea class that uses the UAG codon to encode leucine. Extending our analysis to include other genomes from the Phyllopharyngea class, we identified further changes in Hartmannula sinica and Trochilia petrani where the UAG codon had been reassigned to encode glutamine. Phylogenomics analysis suggests that three lineages within Phyllopharyngea independently reassigned the codon UAG to encode an amino acid. These findings expand our understanding of genetic code evolution and highlight the remarkable diversity of genetic codes employed by ciliates.

McGowan J, Richards TA, Hall N, Swarbreck D (2024)
Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates. PLoS Genet 20(12): e1011512. https://doi.org/10.1371/journal.pgen.1011512

Copyright: © 2024 The authors.
Published by PLoS. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Of course, none of this is a problem for the Theory of Evolution. On the contrary, it is exactly the sort of thing evolutionary biology would lead us to expect. The genetic code is overwhelmingly shared because all known life inherited it from a common ancestor, but it is not immune from later modification. Once a lineage is established, natural selection can only work with what already exists, and under the right circumstances even something as fundamental as stop codons can be reassigned, repurposed and incorporated into a viable biological system.

For creationists, however, this is another example of an argument that works only for as long as the evidence is carefully selected. When the genetic code is broadly similar across life, they claim it points to common design. When it differs, the same argument quietly disappears. But the question remains: if a single designer used the same genetic code as a signature of design, why are there exceptions? And if the exceptions are also designed, then the original claim that sameness points to a common designer loses its force.

Science has no such difficulty. Shared features point to common ancestry; differences point to subsequent evolutionary change. The near-universality of the genetic code and its rare but revealing exceptions are not rival facts needing separate excuses, but parts of the same story: life diversified from common origins, carrying inherited systems with it, while evolution continued to tinker with those systems in different lineages.

So, far from being evidence for a supernatural designer reusing a favourite blueprint, the genetic code is evidence of history. It bears the marks of common descent, contingency and modification over time. As usual, the facts make sense in the light of evolution, while creationism is left trying to explain why its allegedly perfect designer keeps doing things in more than one way.

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