A comparison of the genomes of methane-producing microorganisms (i.e., methanogens) shows that temperature adaptation may not be encoded genomically, but rather is enforced through protein regulation and finer-scale adaptations in amino acids
Peer reviewed publication
TOKYO INSTITUTE OF TECHNOLOGY
IMAGE: A 100X100 MICROMETER FIELD OF VIEW OF AN AGGREGATE OF METHANE-PRODUCING MICROORGANISMS see more
CREDIT: PAULA PRONDZINSKY
Earth’s history has been one of physical extremes – extreme atmospheric conditions, extreme chemical environments, and extreme temperatures. There was a time when the earth was so hot that all water was steam, and the first rains did not fall until the planet had cooled sufficiently. Life appeared soon after, and through it all, life found a way. Today there is life on Earth almost everywhere we look; It is difficult to find places where life does not exist. Life’s remarkable ability to adapt to changing conditions is one of its defining characteristics. Of its many adaptations, one of the most interesting is life’s ability to adapt to different temperatures. All life relies on chemical reactions that are inherently temperature sensitive. Yet life exists across a spectrum of temperatures, from the Antarctic Ice Shelf to the rims of undersea volcanoes. This begs the question, how does life adapt to different temperatures? To get to the bottom of this question, a research team led by Paula Prondzinsky and Shawn Erin McGlynn of the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology recently studied a group of organisms called methanogens.
Methanogens are methane-producing, unicellular microorganisms that belong to a larger domain of the “archaea” (ancient, unicellular organisms that lack a nucleus and are thought to be precursors of eukaryotic cells). As a single physiological group, methanogens can thrive across a range of temperature extremes, from -2.5 oC to 122 oC, making them ideal candidates for studying temperature adaptation.
In this work, researchers analyzed and compared the genomes of different types of methanogens. They divided methanogens into three groups based on the temperatures in which they thrive — thermotolerant (high temperatures), psychrotolerant (low temperatures), and mesophilic (ambient temperatures). They then created a database of 255 genomes and protein sequences from a resource called the Genome Taxonomy Database. Next, they obtained temperature data for 86 methanogens found in laboratory collections from the Database of Growth TEMPeratures of Usual and Rare Prokaryotes. The result was a database that linked genome content to growth temperature.
The researchers then used software called OrthoFinder to create different orthogroups – sets of genes descended from a single gene present in the last common ancestor of the species under consideration. Then they separated these orthogroups into i) nuclear (present in over 95% of species), ii) common (present in at least two species but in less than 95% of organisms), and iii) unique (present only in a single species) . Their analyzes revealed that about a third of the methaogenic genome is shared by all species. They also found that the amount of shared genes between species decreases as evolutionary distance increases.
Interestingly, the researchers found that thermotolerant organisms had smaller genomes and a higher fraction of the nuclear genome. It has also been found that these small genomes are evolutionarily “older” than the genomes of psychotolerant organisms. Because thermotolerant organisms have been found in multiple groups, these results suggest that the size of the genome is more dependent on temperature than evolutionary history. They also suggest that methanogen genomes grew rather than shrunk over the course of their evolution, challenging the idea of ”thermoductive genome evolution,” meaning that organisms remove genes from their genomes as they evolve to locations with higher temperatures.
The researchers’ analyzes also showed that methanogens grow in this wide temperature range without many special proteins. In fact, most of the proteins encoded by their genomes were similar. This led them to consider the possibility of cellular regulation or finer compositional adjustments as the main cause of temperature adjustment. To investigate this, they examined the composition of amino acids – the building blocks of proteins – in the methanogens.
They found that certain amino acids were enriched in certain temperature groups. They also found differences in the composition of amino acids in terms of their proteomic charge, polarity and entropy of unfolding, all of which affect protein structure and hence its ability to function. In general, they found that thermotolerant methanogens have more charged amino acids and functional genes for ion transport that are not present in psychrotolerants. While psychrotolerant organisms are enriched in uncharged amino acids and proteins related to cell structure and motility. However, the researchers could not locate specific features 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.
Overall, “This shows that the very first methanogens, which evolved at a time when conditions on Earth were hostile to life, may have been similar to the organisms we find on Earth today,” explains Paula Prondzinsky. “Our results could point to features and functions present in the earliest microbes, and even provide clues as to whether microbial life arose in hot or cold environments. We could extend this knowledge to understand how life might adapt to other extreme conditions, not just temperature, and even unravel how life might evolve on other planets.”
Reference:
Paula Prondzinsky1,2,*, Sakae Toyoda2, Shawn Erin McGlynn1,3,4*, The Methanogen Core and Pangenome: Conservation and Variability across Biology’s Growth Temperature Extremes, DNA Research, DOI: 10.1093/dnares/dsac048
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550 Tokyo, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, 351-0198 Saitama, Japan
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA
More information
Tokyo Technical Institute (Tokyo Tech) is at the forefront of research and higher education as the leading university of science and technology in Japan. Tokyo Tech researchers excel in areas ranging from materials science to biology, computer science and physics. Founded in 1881, Tokyo Tech hosts over 10,000 undergraduate and graduate students each year who grow into leading scientists and some of the most sought-after engineers in the industry. The Tokyo Tech community embodies the Japanese philosophy of “Monotsukuri” which means “technical ingenuity and innovation” and strives to contribute to society through high-impact research.
The Earth Life Science Institute (ELSI) is one of the ambitious international research centers in Japan, whose goal is to make advances in largely interdisciplinary scientific fields by inspiring the world’s greatest minds to come to Japan and collaborate on the most challenging scientific problems. The main goal of ELSI is to address the origin and co-evolution of earth and life.
The World Premier International Research Center Initiative (WPI) was established in 2007 by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to support the establishment of globally visible research centers in Japan. These institutes promote high research standards and excellent research environments that attract top researchers from all over the world. These centers are highly autonomous, allowing them to revolutionize the conventional methods of research operation and management in Japan.
DIARY
DNA research
DOI
10.1093/dnares/dsac048
METHOD OF RESEARCH
Experimental study
RESEARCH SUBJECT
Not applicable
ARTICLE HEADING
The methanogen core and the pangenome: Conservation and variability across the extreme temperatures of growth in biology
ARTICLE PUBLICATION DATE
February 1, 2023
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