Uncovering the secrets of LUCA, the oldest life form on Earth

Digital representation showing how LUCA was already under attack by viruses even 4.2 billion years ago. Copyright: Science Graphic Design

a University of BristolLife on Earth, which originated from a common ancestor called LUCA, flourished shortly after the planet formed, a study by Harvard University researchers has found.

Through genetic analysis and evolutionary modeling, the researchers determined that LUCA existed about 4.2 billion years ago, revealing it as a complex organism with an early immune system integrated with the oldest ecosystems on Earth.

Genetic map of LUCA and its descendants

Everything alive today descends from a single common ancestor affectionately known as LUCA (Last Universal Common Ancestor).

LUCA is the putative common ancestor from which all modern cellular life, from single-celled organisms like bacteria to giant redwood trees (and us humans), descended. LUCA represents the root of the tree of life before it split into the groups known today, bacteria, archaea, and eubacteria. Modern life evolved from LUCA from different sources: the same Amino acids Used to build proteins in all cellular organisms, the common currency of energy (ATP), and the presence of cellular machinery such as the ribosome and others associated with making proteins from information stored in DNAand even the fact that all cellular life forms use the same DNA as a means of storing information.

Research Methods and the LUCA Era

The team compared all the genes in the genomes of the organisms. Classby counting the mutations that have occurred within their sequences over time since they shared an ancestor in LUCA.

The time of the divergence of some species is known from the fossil record, so the team used a genetic equivalent of the familiar equation used to calculate velocity in physics to work out when LUCA was present. They arrived at the answer that it occurred 4.2 billion years ago, about 400 million years after the formation of the Earth and our solar system.

“We did not expect Luca to be this old, within hundreds of millions of years of Earth’s formation,” said Dr Sandra Alvarez Carretero, co-author of the study from Bristol’s School of Earth Sciences. “However, our results are consistent with modern views of the habitability of the early Earth.”

Physiological insights and evolutionary modeling of LUCA

The team then worked to determine the biology of LUCA by modeling the physiological characteristics of living species through a lineage of life to LUCA. “The evolutionary history of genes is complex because of their exchange between lineages,” explained lead author Dr. Edmund Moody. “We have to use complex evolutionary models to reconcile the evolutionary history of genes with the lineage of species.”

“One of the real advantages here is that we can apply the gene tree and species tree reconciliation approach to such a diverse set of data representing key domains of life such as archaea and bacteria,” said study co-author Dr Tom Williams from Bristol’s School of Biological Sciences. “This allows us to say with some confidence and assess this level of confidence about how LUCA lived.”

The complexities of the LUCA project and its environmental impact

“Our study shows that LUCA was a complex organism, not very different from modern prokaryotes, but what is really interesting is that it clearly had an early immune system, showing that even 4.2 billion years ago, our ancestors were engaged in an arms race with viruses,” said Professor David Pisani, co-author of the study.

“LUCA was clearly exploiting and changing its environment, but it is unlikely to have lived alone,” said co-author Tim Lenton (from the University of Exeter’s School of Geography). “Its waste could have been food for other microbes, such as methanogens, which would have helped create a recycling ecosystem.”

The broader implications of early life study

“The results and methods used in this work will also benefit future studies that investigate in more detail the subsequent evolution of archaea in the light of Earth’s history, including the less studied archaea with their methanogenic representatives,” added co-author Professor Anja Spang (Royal Netherlands Institute for Sea Research).

“Our work brings together data and methods from multiple disciplines, revealing insights into the early Earth and life that could not have been achieved by any one discipline alone,” said co-author Professor Philip Donoghue. “It also shows how quickly an ecosystem could have been established on early Earth. This suggests that life may have flourished in Earth-like biospheres elsewhere in the universe.”

Reference: “The Nature of the Last Global Common Ancestor and Its Impact on the Early Earth System” by Edmund R. R. Moody, Sandra Alvarez-Carretero, Tara A. Mahendrarajah, James W. Clark, Holly C. Bates, Nina Dombrowski, Lenard L. Xanthou, Richard A. Boyle, Stuart Dennis, Shi Chen, Nick Lin, Zheng Yang, Graham A. Shields, Gergely J. Solusi, Anya Spang, David Pisani, Tom A. Williams, Timothy M. Lenton, and Philip C. J. Donoghue, 12 July 2024. Natural ecology and evolution.
doi: 10.1038/s41559-024-02461-1

Scientists from University College London (UCL), Utrecht University, the Centre for Environmental Research in Budapest, and the Okinawa Institute of Science and Technology Graduate University also participated in the study.

The research was funded by the John Templeton Foundation. The views expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.