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How does life thrive in extreme temperatures?

The most heat-tolerant methanogens were found at a deep-sea hydrothermal vent site. Credit: NOAA
The most heat-tolerant methanogens were found at a deep-sea hydrothermal vent site. Credit: NOAA

Life is remarkable for its ability to adapt to changing conditions, including varying temperatures. However, the mechanisms underlying temperature adaptation remain unclear. To unravel this mystery, researchers at the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology have studied methanogens, a group of single-celled microorganisms that produce methane and thrive across a range of temperatures, from -2.5 degrees C to 122 degrees C. Their findings shed light on the genetics of temperature adaptation and could provide clues to the origin of life on Earth and the possibility of life on other planets.

Analyzing Methanogens' Genomes

The researchers compared the genomes of different species of methanogens, dividing them into three groups based on their temperature preferences: thermotolerant (high temperatures), psychrotolerant (low temperatures), and mesophilic (ambient temperatures). They constructed a database of 255 genomes and protein sequences from the Genome Taxonomy Database and obtained temperature data for 86 methanogens from the Database of Growth TEMPeratures of Usual and Rare Prokaryotes. The resulting database linked genome content to growth temperature.

The researchers then used a software called OrthoFinder to establish different orthogroups, sets of genes descended from a single gene present in the last common ancestor of the species under consideration. They segregated these orthogroups into core, shared, and unique genes. Their analyses revealed that about one third of the methaogenic genome is shared across all species. They also found that the amount of shared genes between species decreases with increasing evolutionary distance.

Thermotolerant Methanogens and Genome Size

The researchers found that thermotolerant organisms had smaller genomes and a higher fraction of core genome. These small genomes were also more evolutionarily "ancient" than the genomes of psychrotolerant organisms. These findings indicate that genome size is more reliant on temperature than on evolutionary history. They also suggest that as methanogen genomes evolved, they grew rather than shrank, challenging the idea of thermoreductive genome evolution.

Protein Composition and Temperature Adaptation

The researchers found that methanogens grow across a wide range of temperatures without many special proteins. Most of the proteins encoded by their genomes were similar. This led them to consider the possibility of cellular regulation or finer scale compositional adaptations as the root cause of temperature adaptation.

A 100x100 micrometer field of view of an aggregate of methane-producing microorganisms. Credit: Paula Prondzinsky
A 100x100 micrometer field of view of an aggregate of methane-producing microorganisms. Credit: Paula Prondzinsky

To investigate this, they looked into the composition of amino acids, the building blocks of proteins, in the methanogens. They found that specific amino acids were enriched in particular temperature groups. They also found compositional differences in the amino acids pertaining to their proteome charge, polarity, and unfolding entropy, which affect protein structure and function. Thermotolerant methanogens have more charged amino acids and functional genes for ion transport, which are not present in psychrotolerants. Psychrotolerants are enriched in uncharged amino acids and proteins related to cellular structure and motility.

Gradual Process of Temperature Adaptation

The researchers could not pinpoint specific functions shared by all members of a temperature group, suggesting that temperature adaptation is a gradual process that occurs in fine steps rather than requiring large-scale changes.

Implications for the Origin of Life on Earth and Beyond

The researchers' findings could point toward traits and functions present in the earliest microbes and even hold clues as to whether microbial life originated in hot or cold environments. They could extend this knowledge to understand how life could adapt to other kinds of extreme conditions, not just temperature, and even unravel how life on other planets could evolve.

Journal Information: Paula Prondzinsky et al, The methanogen core and pangenome: conservation and variability across biology's growth temperature extremes, DNA Research (2022). DOI: 10.1093/dnares/dsac048
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