Unlocking the Past: Scientists Recreate Ancient Proteins to Trace Evolution
Key Advancements from The University of Osaka
Researchers at The University of Osaka have pioneered a new method to reconstruct ancestral rhodopsins—light-sensitive proteins—and successfully test them in living bacteria. Their work, detailed in ACS Omega, offers a powerful new tool for understanding the deep evolutionary history of these crucial proteins.
"Rhodopsins all have seven transmembrane domains that are very similar, but their extramembrane domains... vary dramatically. This makes it very challenging to use standard sequence alignment techniques to trace the evolution of rhodopsin sequences from their shared ancestral proteins."
— Lead author Haruto Ishikawa
Solving the Ancestral Puzzle: The ConsistASR Method
The team's new approach, called ConsistASR, overcomes a major hurdle in evolutionary biology: accounting for insertions and deletions in the extramembrane domains. These variable regions, which have historically complicated standard sequence alignment, are now integrated into the reconstruction process, allowing scientists to trace rhodopsin evolution more accurately.
Using this pipeline, the researchers reconstructed and synthesized sequences for two ancient proteins:
- Ancestral schizorhodopsin
- Ancestral heliorhodopsin
These reconstructed genes were then expressed in Escherichia coli bacteria to see if the ancient proteins would still function.
Exciting Experimental Results
The results surpassed expectations. Both ancient proteins assembled correctly in the bacteria, displaying characteristic colors and spectral properties that matched their modern descendants.
"The results were very exciting. Both the ancestral schizorhodopsin sequence and the ancestral heliorhodopsin sequence produced stable, mature proteins in Escherichia coli that had a distinctive color and showed characteristic spectral properties, just like existing rhodopsins."
— Senior author Yasuhisa Mizutani
Functionally, the two proteins showed a key difference:
- Ancestral schizorhodopsin was active, demonstrating light-driven proton-transport activity.
- Ancestral heliorhodopsin was stable and properly folded, but did not pump ions.
A New Tool for the Research Community
This breakthrough provides a valuable resource for other scientists. The ConsistASR pipeline is now publicly available, enabling researchers to reconstruct and experimentally test other ancestral protein sequences.
"Our findings show that sequence reconstruction that takes insertions and deletions into account can successfully generate full-length ancestral rhodopsins that can be experimentally produced and tested."
— Haruto Ishikawa
By merging computational reconstruction with experimental validation, this method opens a new window into the functional evolution of diverse protein families.