Cornell scientists have created an evolutionary model that connects organisms living in today’s oxygen-rich atmosphere billions of years back to a time when Earth’s atmosphere was low in oxygen, by analyzing of ribonucleotide reductases (RNR), a family of proteins used by all free-living people. organisms and many viruses to repair and replicate DNA.
“By understanding the evolution of these proteins, we can understand how nature adapts to environmental changes at the molecular level. In turn, we also learn about our planet’s past,” said Nozomi Ando, associate professor of chemistry and chemical biology in the Faculty of Arts and Sciences and corresponding author of the study. “Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade” published in eLife Digest on October 4.
Co-first authors of the study are Audrey Burnim and Da Xu, PhD students in chemistry and chemical biology, and Matthew Spence, Research School of Chemistry, Australian National University, Canberra. Colin J. Jackson, Professor of Chemistry at the Australian National University, Canberra, is a corresponding author.
This undertaking involved a large data set of 6,779 RNR sequences; the phylogeny took several high-performance computers a total of seven months (1.4 million CPU hours) to compute. Made possible by advances in computing, the approach opens up a new way to study other diverse protein families that have evolutionary or medical significance.
RNRs have adapted to environmental changes over billions of years to retain their catalytic mechanism because of their essential role for all DNA-based life, Ando said. His lab studies protein allostery: how proteins can change activity in response to the environment. The evolutionary information in a phylogeny gives us a way to study the relationship between the primary sequence of a protein and its three-dimensional structure, dynamics and function.
RNRs are thought to have ancient origins because they catalyze the reaction of turning RNA building blocks into DNA building blocks, Ando said, making them ideal for finding a molecular record.
“This chemistry would have been necessary to move from the hypothetical RNA world to the DNA/protein world we live in today,” Ando said. “Based on the cofactors used by the RNRs, it is also clear that this family of enzymes has adapted to the increased oxygen in Earth’s atmosphere. Both transitions took place billions of years ago.” .
When scientists build a phylogeny of a protein family, they calculate what the currently existing sequences looked like, Ando said. In this process, they have to estimate what happened in the past to get the sequences that exist now.
Burnim said the researchers calculated the RNR phylogeny by assembling a dataset of more than 100,000 sequences and retaining a computationally tractable dataset of 6,779 sequences maintaining the diversity of the entire family. The length of the sequences ranges from about 400 to 1,100 amino acids. Using models of how amino acids mutate, they compared the sequences to each other to determine when they diverged.
Based on this work, the researchers discovered a new and distinct group of RNRs that would explain how two different adaptations to oxygen on Earth arose within this family of proteins.
They used small-angle X-ray scattering at Cornell’s High Energy Synchrotron Source, cryogenic electron microscopy at the Cornell Center for Materials Research, and the artificial intelligence program AlphaFold2 to study Synechococcus phage RNR S-CBP4, a virus that infects a cyanobacterium, Xu said.
“When we calculated the RNR family tree, it turned out that there was a branch of RNR that we didn’t know was a different lineage,” Ando said. “This branch included sequences from marine organisms, including cyanophages. Our characterization of one of the sequences suggests that there was an early adaptation to oxygen. The cyanophage connection was interesting because it suggests that their hosts ( cyanobacteria) were at the same time, and cyanobacteria are credited with oxygenating the Earth.”
The findings support the idea that molecular adaptations to oxygen occurred long before the planet’s large-scale environmental changes, according to the geochemical record, Ando said.
This first unified evolutionary model for all classes of RNR could provide many future directions for the field, Xu said.
Ando plans to use the same approach to study how enzymes with the same overall structure evolved to catalyze completely different chemical reactions.
This research was supported by the National Science Foundation, the National Institute of General Medical Sciences, the National Institutes of Health, and the Empire State Development Corporation of New York State.
Kate Blackwood is a writer in the Faculty of Arts and Sciences.
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