Finding extraterrestrial life forms with the help of ancient microbes

Ancient microbes captured light using light-capturing protein


The relationship between life and the environment it inhabits holds many clues about how the planet became habitable over the years. Planetary habitability is strongly influenced by solar insolation and photon radiance flux, which couple planetary and stellar evolution to the persistence of life.

Many of Earth’s geochemical proxy records are incomplete. This is why there are limitations on reconstructing planetary and solar factors that have influenced habitability and the co-evolution of life and its environments.

In a recent study published in the journal Molecular Biology and Evolution, researchers found that ancient microbes derived plentiful energy from the sun without the complex biomolecules required for photosynthesis with the help of protein Rhodopsins. They reconstructed the evolution of protein, and these efforts could help to recognize signs of life on other planets, whose atmospheres may more closely resemble our pre-oxygen planet.

Ancient microbes without ozone layer

The ancient microbes, including bacteria and single-celled organisms called archaea, inhabited a primarily oceanic planet without an ozone layer to protect them from the sun’s radiation. These microbes evolved rhodopsins which are proteins with the ability to turn sunlight into energy and then use them to power cellular processes.

“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,” said UC Riverside astrobiologist Edward Schwieterman, who is co-author of a study describing the research.

Significance of Rhodopsins

Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors. They are also widely distributed among modern organisms and environments like saltern ponds, which present a rainbow of vibrant colors.

“Photosensitive proteins are key intermediaries that connect intracellular chemical states, extracellular substrate availability, and solar irradiance. These biomolecules constitute a promising system for tracking ancient physical parameters that are not directly recorded in the geologic record. All known phototrophic metabolisms on Earth rely on one of three energy-converting pigments which transform light energy into chemical energy. These pigments include chlorophylls, bacteriochlorophylls, and retinal. Retinal-based pigment proteins, known as rhodopsins, have been found in Archaea, Bacteria, Eukarya, and giant viruses.” Study mentions.

Researchers used machine learning to analyze rhodopsin protein sequences from all over the world and tracked how they evolved over time. Then, they created a type of family tree that allowed them to reconstruct rhodopsins from 2.5 to 4 billion years ago and the conditions that they likely faced.

“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,” said University of Wisconsin-Madison astrobiologist and study lead Betul Kacar.

“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 absorb blue, green, yellow, and orange light and can appear pink, purple, or red by virtue of the light they are not absorbing or complementary pigments. However, according to the team’s reconstructions, ancient rhodopsins were tuned to absorb mainly blue and green light.

Since ancient Earth did not yet have the benefit of an ozone layer, the research team theorizes that billions of years-old microbes lived many meters down in the water column to shield themselves from intense UVB radiation at the surface.

Blue and green light best penetrates water, so it is likely that the earliest rhodopsins primarily absorbed these colors. “This could be the best combination of being shielded and still being able to absorb light for energy,” Schwieterman said.

After the Great Oxidation Event, more than 2 billion years ago, Earth’s atmosphere began to experience a rise in the amount of oxygen. Additional oxygen and ozone in the atmosphere caused rhodopsins to evolve to absorb additional colors of light.

Rhodopsins today are able to absorb colors of light that chlorophyll pigments in plants cannot. Though they represent completely unrelated and independent light capture mechanisms, they absorb complementary areas of the spectrum.

“This suggests co-evolution, in that one group of organisms is exploiting light not absorbed by the other,” Schwieterman said. “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.”

The team is hoping to resurrect model rhodopsins in a laboratory using synthetic biology techniques.

“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.

Ultimately, the team is pleased about the possibilities for research opened up by the techniques they used for this study.

Limitation of study

Since other signs of life from the deep geologic past need to be physically preserved and only some molecules are amenable to long-term preservation, there are many aspects of life’s history that have not been accessible to researchers until now.

Importance of study

“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 hopes their research may help search for life signs on other planets.

“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.

Journal Reference

  1. Cathryn D. Sephus, Evrim Fer, Amanda K. Garcia, Zachary R. Adam, Edward W. Schwieterman, Betul Kacar. Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins. Molecular Biology and Evolution, Volume 39, Issue 5, May 2022, msac100, DOI: 10.1093/molbev/msac100


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