Researchers examine ancient microbes to find life beyond earth

Researchers have reproduced what life was like for some of the oldest species on Earth using light-capturing proteins found in living microorganisms. These initiatives may enable everyone to spot life in distant worlds, whose atmospheres mirror the pre-oxygen planet more closely.

Researchers examine ancient microbes to find life beyond earth
Rendering of the process by which ancient microbes captured light with rhodopsin proteins. Image Credit: Sohail Wasif/UCR

The oldest known life existed in an ocean-dominated world without an ozone layer to shield it from the sun’s radiation. These early life forms included bacteria and single-celled animals known as archaea. Rhodopsins, proteins with the capacity to convert sunlight into energy, were developed by these bacteria and are now used to fuel cellular functions.

On early Earth, energy may have been very scarce. Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis.”

Edward Schwieterman, Study Co-Author, Astrobiologist, UC Riverside

Rods and cones in human eyes that let humans discriminate between light and dark and perceive color is related to rhodopsins. They are also abundant in contemporary animals and settings, such as saltern ponds, which display a rainbow of vivid hues.

The research group examined rhodopsin protein sequences from all over the world and followed the evolution of these sequences over time using machine learning. As a result, they were able to rebuild rhodopsins from 2.5 to 4 billion years ago and the environments they probably lived in.

Their results are thorough in a paper published in the journal Molecular Biology and Evolution.

Life as we know it is as much an expression of the conditions on our planet as it is of life itself. We resurrected ancient DNA sequences of one molecule, and it allowed us to link to the biology and environment of the past.”

Betul Kacar, Study Lead and Astrobiologist, University Of Wisconsin-Madison

It’s like taking the DNA of many grandchildren to reproduce the DNA of their grandparents. Only, it’s not grandparents, but tiny things that lived billions of years ago, all over the world,” Schwieterman said.

Modern rhodopsins can seem pink, purple, or red due to the light they are not catching or complementary pigments. They take blue, green, yellow, and orange light. However, the team’s reconstructions suggest that early rhodopsins were tuned to mostly absorb blue and green light.

The research group hypothesizes that billions-of-years-old bacteria lived many meters below the water column to protect themselves from high UVB radiation at the surface because ancient Earth did not yet have the advantage of an ozone layer.

Since blue and green light may best pass through water, it is most likely that the first rhodopsins collected these hues predominantly. “This could be the best combination of being shielded and still being able to absorb light for energy,” Schwieterman said.

More than two billion years ago, the Great Oxidation Event caused an increase in oxygen levels in the Earth’s atmosphere. Rhodopsins adapted to absorb more colors of light as the atmosphere’s oxygen and ozone levels increased.

Today’s rhodopsins can capture colors of light that plant chlorophyll pigments cannot. They take complementing parts of the spectrum while being fully unrelated and distinct light capture systems.

This suggests co-evolution, in that one group of organisms is exploiting light not absorbed by the other. This could have been because rhodopsins developed first and screened out the green light, so chlorophylls later developed to absorb the rest. Or it could have happened the other way around.”

Edward Schwieterman, Study Co-Author, Astrobiologist, UC Riverside

In the future, the team plans to use synthetic biology methods to revive model rhodopsins in a laboratory.

We engineer the ancient DNA inside modern genomes and reprogram the bugs to behave how we believe they did millions of years ago. Rhodopsin is a great candidate for laboratory time-travel studies,” Kacar said.

In the end, the team is happy with the research avenues that their methods for this study have opened up. Many parts of the evolution of life have not been available to scholars until now because other traces of life from the deep geologic history need to be physically maintained and only particular molecules are susceptible to long-term conservation.

Our study demonstrates for the first time that the behavioral histories of enzymes are amenable to evolutionary reconstruction in ways that conventional molecular biosignatures are not,” Kacar said.

The team also aims to use what they have discovered about the behavior of early Earth species to examine the skies for evidence of extraterrestrial life.

Early Earth is an alien environment compared to our world today. Understanding how organisms here have changed with time and in different environments is going to teach us crucial things about how to search for and recognize life elsewhere,” Schwieterman said.

Source:
Journal reference:

Sephus, C. D., et al. (2022) Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins. Molecular Biology and Evolution. doi.org/10.1093/molbev/msac100.

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