Friday, 10 June 2022

Common Origins - How Modern Chromatin Shows the Common Ancestry of All Eukaryotes

Ancyromonas sigmoides, an understudied microbe that holds enormous promise for investigations into the origin of eukaryotes

Credit: Naoji Yubuki
Chromatin originated in ancient microbes one to two billion years ago | Centre for Genomic Regulation

For some bizarre reason, creationists often claim that the science of epigenetics somehow falsifies Darwinian evolution because, so they claim, it shows how genetic changes acquired after birth can be passed on to the next generation, although how that falsifies the observable fact that allele frequency in a population changes over time is never explained when the rehearsed talking points are regurgitated on cue.

It is ironic then, that, according to research by scientists at the Center for Genomic Regulation (CRG) at the Barcelona Institute of Science and Technology (BIST), Barcelona, Spain, a vital component of the epigenetic system, the chromatin, or histones, around which DNA is wrapped and which exerts a control over which genes are expressed in the specialised cells of multicellular organisms, had its origins in remote ancestral prokaryote organism some 1-2 billion years ago and so is evidence of common ancestry.

To make matters worse for creationists, the evidence suggests that histones probably evolved as defensive structures in response to selective environmental pressures by genetic parasites such as viruses, in classical Darwinian evolution by natural selection and the inevitable arms races.

As the CRG news release explains:
In almost every human cell, two metres-long DNA has to fit within a nucleus that is just 8 millionths of a meter wide. Like wool around a spool, the extreme space challenge requires DNA to wrap around structural proteins called histones. This coiled genetic architecture, known as chromatin, protects DNA from damage and has a key role in gene regulation.

Our results underscore that the structural and regulatory roles of chromatin are as old as eukaryotes themselves. These functions are essential for eukaryotic life — since chromatin first appeared, it's never been lost again in any life form. We are now a bit closer to understanding its origin, thanks to the power of comparative analyzes to uncover evolutionary events that occurred billions of years ago.

Dr. Xavier Grau-Bové, first author
Centre for Genomic Regulation (CRG)
Barcelona Institute of Science and Technology (BIST) And Universitat Pompeu Fabra (UPF) Barcelona, Catalunya, Spain
Histones are present in both eukaryotes, living organisms that have specialized cellular machinery such as nuclei and microtubules, and archaea, another branch of the tree of life consisting of single-celled microbes that are prokaryotic, meaning they lack a nucleus.

In eukaryotic cells, histones are modified by enzymes, continuously shapeshifting the genomic landscape to regulate gene expression and other genomic processes. Despite this fundamental role, the exact origin of chromatin has been shrouded in mystery.

Researchers at the Center for Genomic Regulation (CRG) now reveal that nature's storage solution first evolved in ancient microbes living on Earth between one and two billion years ago. The study is published today in the journal Nature Ecology and Evolution.

To go back in time, the researchers used information written in the genomes of modern organisms, organizing life forms according to the evolution of genes and proteins linked to chromatin. They studied thirty different species obtained from water samples in Canada and France. The microbes were identified thanks to modern gene-sequencing technologies that allow the identification of species by filtering DNA. They were subsequently grown in the lab for proteomic and genome sequencing.

Viruses and transposable elements are genome parasites that regularly attack DNA of single-celled organisms. This could have led to an evolutionary arms-race to protect the genome, resulting in the development of chromatin as a defensive mechanism in the cell that gave rise to all known eukaryotic life on Earth. Later on, these mechanisms were co-opted into elaborate gene regulation, as we observed in modern eukaryotes, particularly multicellular organisms.

Dr. Arnau Sebe-Pedrós, senior author
Centre for Genomic Regulation (CRG)
Barcelona Institute of Science and Technology (BIST)
And Universitat Pompeu Fabra (UPF)
Barcelona, Catalunya, Spain
The researchers found that prokaryotes lack the machinery necessary to modify histones, suggesting archaeal chromatin at the time could have played a basic structural role but did not regulate the genome. In contrast, researchers found ample evidence of proteins that read, write and erase histone modifications in early diverging eukaryotic lineages such as the malawimonad Gefionella okellyi, the ancyromonad Fabomonas tropica, or the discoban Naegleria gruberi , microbes that had not been sampled until now.

Using the sequence data, the researchers reconstructed the repertoire of genes held by the Last Eukaryotic Common Ancestor, the cell that gave rise to all eukaryotes. This living organism had dozens of histone-modifying genes and lived between one and two billion years ago on Earth, which is itself estimated to be 4.5 billion years old. The authors of the study hypothesise that chromatin evolved in this microbe as a result of selective pressures in the primordial environment of Earth.

According to the authors of the study, future research could look at the evolution of histone-modifying enzymes in Asgardian archaea, microbes named after a mythological region inhabited by Norse gods that are often described as an evolutionary stepping stone between archaea and eukaryotes. The researchers found evidence that some species of Asgardian microbes, such as Lokiarchaeota , have histones with eukaryotic-like features, and could be the result of convergent evolution.
Histones then have their origins in the remote past when prokaryote organisms had been evolving for some 2 billion years before giving rise to the eukaryote single-celled organisms that in turn gave rise to multicellular organisms, and have since been repurposed to control the expression of particular genes according to the speciality of the cells in which they occur - an essential step in complex, multicellular organisms, which have inherited their method of replication from single-celled ancestors and so replicate the entire genome every time, regardless of which fragments of it are going to be needed.

This necessity to have a complex mechanism to regulate gene expression in multicellular organisms is itself evidence of unintelligent design, since it uses a highly complex solution for a problem that would never have been designed by an intelligent designer, which could have arranged things so that specialised cells get only the genes they needs, so avoiding all that waste in replicating the whole genome, and incidentally running the significant risk of it going wrong and giving rise to cancer. Avoidable complexity and risk and prolific waste - the hallmarks of mindless, unintelligent, unplanned, utilitarian evolution and the antithesis of good, intelligent design.

Sadly, the researchers' paper in Nature Ecology & Evolution is behind an expensive firewall but the abstract is available here. In it the authors say:
We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
Just another example of how the use by creationist frauds of an emerging science to misinform and fool their target dupes in creationist cults, is coming back to bite them. What they have fooled them into believing somehow refutes Darwinian evolution, is turning out to provide some of the best evidence for common ancestry in the remote past, in the early years of life on Earth, and this is being revealed quite casually and incidentally by scientists who are simply discovering the facts. As always, the fact fail to support the infantile superstitions of Bronze Age hill farmers.
Reference: Grau-Bové, X., Navarrete, C., Chiva, C. et al.
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution.
Nat Ecol Evol (2022). https://doi.org/10.1038/s41559-022-01771-6

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