The origins of life and the question of humanity’s place in the universe have long intrigued scientists. To explore these questions, researchers often turn to molecular “fossils,” which are ancient structures found across all living organisms.
A recent study by evolutionary biochemists and protein historians has raised new questions about one such molecular fossil within an ancient protein family. The central issue is whether a simple structure found in every organism represents a foundational element for modern biological complexity or merely a remnant that has survived through time. The answers could affect how scientists interpret the beginnings of biology.
Phosphorus is a key chemical element in life, playing roles in genetic material, metabolic reactions, and enzyme regulation. Phosphorus compounds, particularly phosphate, possess unique chemical properties that make them vital for biological processes. According to F.H. Westheimer, phosphates are chemically capable of “do almost everything.” This versatility leads many researchers to focus on phosphorus when searching for signs of life beyond Earth.
Proteins enable organisms to use phosphates effectively. Through phosphorylation—the addition of phosphate groups—proteins can perform essential functions not possible with their basic building blocks alone. Scientists believe that phosphate binding was among the earliest biological functions on Earth.
One group of proteins known as P-loop NTPases is present throughout the tree of life and plays roles in cellular communication and energy storage. These proteins share a motif called a P-loop, which binds phosphate by forming an amino acid nest around it. Every organism contains multiple families of P-loop NTPases; humans have about 5,000 copies according to rough estimates from genome analysis.
Research from 2012 indicated that even isolated P-loops could bind phosphate without their larger protein structures, suggesting they may have functioned before complex proteins evolved.
Margaret Oakley Dayhoff proposed in 1966 that large proteins originated from smaller peptides through duplication and fusion over time—a hypothesis that continues to influence research into protein evolution.
Inspired by Dayhoff’s ideas, researchers used computer models to compare natural P-loops with control loops composed of identical amino acids arranged differently. They discovered both types could form temporary nests within proteins, challenging the belief that only specific sequences like those in P-loops are responsible for this ability.
The findings suggest that while P-loops serve as molecular fossils, their original forms may be obscured by evolutionary changes over billions of years. Further experiments showed environmental factors like solvent type can influence nest formation in these proteins.
The authors argue for caution when interpreting molecular fossils—much like archaeologists approach physical fossils—to avoid misrepresenting early protein evolution and life’s origins.
“In resetting the field’s broader understanding of how these crucial proteins emerged, scientists are poised to start rewriting our own evolutionary history on this planet.”
This article was originally published under a Creative Commons license from The Conversation.
