|Ancyromonas sigmoids, an unstudied microbe with enormous potential for research into the origins of eukaryotes / Credit: Naoji Yubuki
In nearly every human cell, DNA two meters long must fit inside a nucleus no more than 8 millionths of a meter wide. Like the wool around a spool, the extreme space challenge requires DNA to wrap around structural proteins called histones. This coiled genetic structure, known as chromatin, protects DNA from damage and has a key role in gene regulation.
Histones are found in both eukaryotes, organisms that have specialized cellular machineries such as nuclei and microtubules, and archaea, another branch of the tree of life made up of unicellular prokaryotic microbes, meaning they lack a nucleus.
In eukaryotic cells, histones are modified by enzymes, constantly changing the shape of the genetic landscape to regulate gene expression and other genetic processes. Despite this primary role, the exact origin of chromatin is shrouded in mystery.
Researchers at the Center for Genomic Regulation (CRG) now reveal that a natural storage solution first evolved in ancient microbes that lived on Earth between 1 and 2 billion years ago. The findings were published in the journal Nature Ecology and Evolution today.
To go back in time, the researchers used information written into the genomes of modern organisms, organizing life forms according to the evolution of genes and chromatin-related proteins. They looked at thirty different species found in water samples from Canada and France. Microbes have been identified thanks to modern genetic sequencing techniques that allow species identification by DNA filtering. They were subsequently cultured in the laboratory for genome and protein sequencing.
The researchers found that prokaryotes lacked the machinery needed to modify histones, indicating that primitive chromatin at that time could have played an essential structural role but did not regulate the genome. In contrast, the researchers found ample evidence for proteins that read, write, and erase histone modifications in divergent early eukaryotic strains such as Malawimonad Gefionella kelly, ancyromonad Fabomonas Tropica, or Discoban Naegleria gruberi, microbes that have not yet been sampled.
"Our findings show that chromatin's structural and regulatory roles are as old as eukaryotes. These functions are essential for eukaryotic life - since chromatin first appeared, it has not been lost again in any life form," says Dr. Xavier Grau-Bové, Post-Researcher Ph.D. at CRG and first author of the study. "We are now a little closer to understanding its origin, thanks to the power of comparative analyzes to uncover evolutionary events that occurred billions of years ago."
Using the sequence data, the researchers reconstructed the repertoire of genes held by the last common ancestor of eukaryotes, the cell that gave rise to all eukaryotes. This organism had dozens of histone-modifying genes and lived between one and two billion years on Earth, which itself is estimated to be 4.5 billion years old. The study authors hypothesize that chromatin evolved in this microbe as a result of selective pressures in Earth's primitive environment.
"Viruses and transmissible elements are genome parasites that regularly attack the DNA of single-celled organisms," says Dr. Arnau Sepe Pedro, a CRG researcher and senior author of the study. This may lead to an evolutionary arms race to protect the genome, leading to the development of chromatin as a defense mechanism in The cell that gave rise to all eukaryotic organisms on Earth. Later, these mechanisms were selected for detailed gene regulation, as we observe in modern eukaryotes, in particular multicellular organisms."
According to the study authors, future research could look at the evolution of histone-modifying enzymes in Asgardian archaea, Microbes named after a mythical region inhabited by Norse deities, which is frequently 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 eukaryote-like properties, and they could be the result of convergent evolution.
The study is the result of a research project that began eight years ago. Led by CRG researchers, the work is based on the collaboration of the CRG-UPF Proteomics Unit, the Institute for Biologia Evolutiva (CSIC-UPF), Paris-Saclay University, the University of Montreal, and the University of Vienna.
Xavier Grau-Bové, Cristina Navarrete, Cristina Chiva, Thomas Pribasnig, Meritxell Antó, Guifré Torruella, Luis Javier Galindo, Bernd Franz Lang, David Moreira, Purificación López-Garcia, Iñaki Ruiz-Trillo, Christa Schleper, Eduard Sabidó, Arnau Sebé-Pedrós. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nature Ecology & Evolution, 2022; DOI: 10.1038/s41559-022-01771-6