A comparison of the genomes of methane-producing microorganisms (i.e., methanogens), reveals that temperature adaptation might not be genomically encoded, but rather enforced through protein regulation and finer scale adaptations in amino acids
TOKYO INSTITUTE OF TECHNOLOGY
The history of the Earth 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 all the water was vapor, and the first rain only fell once the planet cooled enough. Soon after, life emerged and through it all, life has found a way. Today life is found almost everywhere on Earth we have looked; it is difficult to find places where life does not exist. The remarkable ability of life to adapt to variable conditions is one of its defining characteristics. Of its many adaptations, the ability of life to adapt to varying temperatures is one of the most interesting. All of life relies on chemical reactions, which are by nature sensitive to temperature. And yet, life exists across a spectrum of temperatures, from the Antarctic ice shelf to the edges of submarine volcanoes. This begs the question, how does life adapt to different temperatures? To attempt to unravel this question, a research team, led by Paula Prondzinsky and Shawn Erin McGlynn of the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology, recently investigated a group of organisms called methanogens.
Methanogens are methane-producing, single-celled microorganisms that belong to a larger domain of “Archaea” (ancient, single-celled organisms that do not have cell nuclei and are thought to have been the predecessor to 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 to study temperature adaptation.
In this work, the researchers analysed and compared the genomes of different species of methanogens. They divided the methanogens into three groups based on the temperatures they thrived in—thermotolerant (high temperatures), psychrotolerant (low temperatures), and mesophilic (ambient temperatures). They then constructed a database of 255 genomes and protein sequences from a resource called the Genome Taxonomy Database. Next they obtained temperature data for 86 methanogens which are in laboratory collections from the Database of Growth TEMPeratures of Usual and Rare Prokaryotes. The result was a database which linked genome content to growth temperature.
After that, the researchers 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 then segregated these orthogroups into i) core (present in over 95% of the species), ii) shared (present in at least two species but in less than 95% of the organisms), and iii) unique (present only in a single species). 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.
Interestingly, the researchers found that thermotolerant organisms had smaller genomes and a higher fraction of core genome. These small genomes were also found to be more evolutionarily “ancient” than the genomes of psychrotolerant organisms. Since thermotolerant organisms were found in multiple groups, these findings indicate that the size of the genome is more reliant on temperature than on evolutionary history. They also suggest that as methanogen genomes evolved, they grew rather than shrank, which challenges the idea of “thermoreductive genome evolution,” i.e., that organisms remove genes from their genomes as they evolve into higher temperature locations.
The researchers’ analyses also showed that methanogens grow across this wide range of temperatures 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 scale compositional adaptations as the root cause of temperature adaptation. 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—all of which affect protein structure, and thereby its ability to function. In general, they found that thermotolerant methanogens have more charged amino acids and functional genes for ion transport, which are not present in psychrotolerants. Whereas psychrotolerants organisms are enriched in uncharged amino acids and proteins related to cellular structure and motility. However, the researchers could not pinpoint specific functions shared by all members of a temperature group, suggesting that temperature adaptation is a gradual process which occurs in fine steps rather than requiring large scale changes.
Altogether, “This indicates that the very first methanogens, which evolved at a time when the conditions on the Earth were hostile to life, may have been similar to the organisms we find on present day Earth,” explains Paula Prondzinsky. “Our 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. We 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.”
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
Tokyo Institute of Technology (Tokyo Tech) stands at the forefront of research and higher education as the leading university for science and technology in Japan. Tokyo Tech researchers excel in fields ranging from materials science to biology, computer science, and physics. Founded in 1881, Tokyo Tech hosts over 10,000 undergraduate and graduate students per year, who develop into scientific leaders and some of the most sought-after engineers in industry. Embodying the Japanese philosophy of “monotsukuri,” meaning “technical ingenuity and innovation,” the Tokyo Tech community strives to contribute to society through high-impact research.
The Earth-Life Science Institute (ELSI) is one of Japan’s ambitious World Premiere International research centers, whose aim is to achieve progress in broadly inter-disciplinary scientific areas by inspiring the world’s greatest minds to come to Japan and collaborate on the most challenging scientific problems. ELSI’s primary aim is to address the origin and co-evolution of the Earth and life.
The World Premier International Research Center Initiative (WPI) was launched in 2007 by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to help build globally visible research centers in Japan. These institutes promote high research standards and outstanding research environments that attract frontline researchers from around the world. These centers are highly autonomous, allowing them to revolutionize conventional modes of research operation and administration in Japan.
METHOD OF RESEARCH
SUBJECT OF RESEARCH
The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes
ARTICLE PUBLICATION DATE
The history of the Earth has been one of physical extremes—extreme atmospheric conditions,
BUT…always remember the dooming looming-
Big wet ‘a stay of execution’ for Aussie environment (msn.com)
A very extrem situation for existing life was the first appearance of oxygene in the atmosphere.
“…might not be genomically encoded, but rather enforced through protein regulation and finer scale adaptations in amino acids”
The striking thing about post-modern science is the more complex the matter in hand – climate, genomes etc – the more certain they are that they and only they understand it. Biologists and ecologists are firmly convinced that species and nature are doomed unless the human steps in to help – they cannot adapt or evolve. Nature just can’t cope….
You sort of nailed it…
This being a perfect example of modern science= never ending excursions into a Minutia Mine and returning, breathless with faux excitement, with truckloads of Trivia
As Ron alludes to below, it all hinges on the definition of Extreme = something which has 8 Billion (and counting) differing definitions.
If it/anything was **that** extreme, there wouldn’t be any life there – it’s all just so perfectly circular. All they’ve really noticed is that ‘some things‘ are different from ‘some other things‘
That of course (as applied to people) is the very staff of life for politicians, bureaucrats, climate scientists and not least (as we witness around here oft enough) Lawyers
And those parasites, getting out of bed every day, noticing that “today is different from yesterday” then charging time/money/resource for doing that: are killing their host.
There are now too many of them.
I guess you have to be a misanthrope at heart…
Empty half the Earth of its humans. It’s the only way to save the planet
If we managed urbanisation properly, we could nearly remove ourselves from a considerable percentage of the the planet’s surface.
They will have to be green cities, sure. We will have to have decarbonised transport and energy production, white roofs, gardens in every empty lot, full-capture recycling, and all the rest of the technologies of sustainability we are already developing. That includes technologies we call law and justice – the system software, so to speak. Yes, justice: robust women’s rights stabilise families and population. Income adequacy and progressive taxation keep the poorest and richest from damaging the biosphere in the ways that extreme poverty or wealth do. “
I wonder if there is a relationship between the metagenetic impact of multi-generations of extreme-climate fear and the evolution of human intellect and ability to cope? . Not worried, if any humans are left on the planet, Biotech will be able to adapt via Crispr Cas9 the human genome to increase intellect and coping ability as needed.
Extreme climate means we need transhumant to evolve a transnature or stuff is going to become inhospitable quickly. Got to laugh at this stuff.
Instead of all this scientific study why don’t they just ask retirees from Chicago how they adapted to retirement in Florida? Looks to me like that contains a clue (Sparky). Sorry.
Why do Europeans fly south for their holidays? It’s a mystery.
Imagine that life forms can adapt, even thrive, with changes in temperature. No way. We’re all gonna die if it gets a degree or two warmer. How about if it gets cooler? Huh? Folks in Fort Lauderdale go nuts if it gets below 50 deg F. The iguanas fall outta trees when it gets down to 40 deg F every coupla years.
There are five to ten nights/year in Fort Lauderdale where I get to wear the Pendleton shirts I brought with me from colder climes.
Charles, you’re obviously younger than me because I gave my Pendleton shirts to the Salvation Army 20 years ago. Just saying.
Well, I’m old enough to be on Medicare. No reason to give up the best shirts in the world. Been wearing for over four decades.
Glad to here you can still fit into them! I still have all 6 of mine, (1971-1976). They are a in demand vintage clothing item right now. Prices range $35 to $1,000 depending on size pattern colors and condition. Unfortunately, my son is a long distance runner and doesn’t have the upper body to wear them.
@Ctm and Ron
We’re in the Panhandle and have not abandoned our heavy gear because we’re reverse snowbirds that go up to high Colorado in May and return in October. It also gets cold here, unlike the “real Florida” people think of – hell, it got a bit below 30 deg just last week!
Only reasons humans survived cold after evolving in Africa is they learned to make a fire. They didn’t evolve as 99.9% of the other living organisms populating the planet.
I often wonder what the same folks on the doom train would be doing if the models forecast a few degrees colder, sort return to the Little Ice Age and another degree or two. Hmmm.
It’s amazing to know that there exist Archeae freezing at +80°C 😀
Generally good, but still doesn’t solve well known problems.
“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—all of which affect protein structure, and thereby its ability to function.”
How does a frog catch a fly when the frog is cold? Speaking from memory, back in the day, people studied Rhodopsin and found an enthalpy/entropy covariance maintained the free energy of activation of this protein which meant that evolutionarily-separated frogs could react at the same speed in warm or cold environments.
I suspect the protein-folders haven’t made a lot of progress since I stopped watching, but at least they aren’t telling us how to run the world’s economic and political systems.
“thermoreductive genome evolution,” i.e., that organisms remove genes from their genomes as they evolve into higher temperature locations. – To me, this is counter-intuitive.
It would seem more logical that organisms would evolve in a given environment and add genes to adapt to new conditions, creating more complexity. Like government regulations and British motorcycles of the 60’s.
As I understand it, it is very rare for genes to be removed, hence “junk” DNA.
It may be that genes are added to the genome to cope with lower temperature locations.
“Paula Prondzinsky and Shawn Erin McGlynn of the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology”
I guess a different department is looking after the Non-Earth-Life Sciences. You know that idiots have taken over universities by the wordy titles and names of departments. They feel the need to fill the vacuum.
Soil responses and plant epigenetic responses to CO2 lag emissions/concentration increases.
Biosphere uptake lags emissions/concentrations substantially. The land biosphere takes in an increasing portion of emissions every year. Soil and microbial effects lag, also epigenetic responses. Every year the biosphere takes in more. In the 90s it was about 25% of emissions, today it’s close to 30%, even as emissions went up substantially. This also makes the land better at handling water.
See full ￼￼🧵 https://mobile.twitter.com/aaronshem/status/1126891477857198081
Back in 2019, my wife and I stayed at Yellowstone National Park for a few days, and did several lengthy hikes. I highly recommend it to anyone interested in nature, because as many places as I’ve visited, this was the most amazing.
Throughout the park, one finds large, shallow pools of water whose shallowest floors are banded with brilliant colors – all of the colors of the rainbow, but much more vivid. At first I thought these must be minerals. I learned very quickly that they were the colors of living microorganisms. The pools of water were hot, nearly boiling hot. Further, they were extremely acidic, with a pH lower (more acidic) than the acid in a lead-acid battery. These thermo-acidophile bacteria flourish throughout the park, in conditions lethal to every form of life we encounter elsewhere. In fact, there’s a book entitled Death In Yellowstone that seems to be required reading for park visitors, and much of it deals with people who have met their end in one of these “thermal features.”
I’ve spent lots of time since wondering how (and why) life evolved to not only survive, but also flourish in such environs. It always takes me back to an article posted in WUWT some time ago about a spot in the Pacific Ocean where an underwater volcanic vent was making the local sea so acidic that human divers in wet suits couldn’t approach too closely – it burned their skin too badly – but all kinds of sea life, from weeds through sharks, lived there unfazed.
As a result, I’m not too concerned about a slight decrease in the alkalinity or even slighter increase in temperature of the oceans due to CO2 in the atmosphere.
Slightly off topic but this statement intrigued me.
How did they determine that without using circular reasoning? It would be interesting to find out.
“This indicates that the very first methanogens, which evolved at a time when the conditions on the Earth were hostile to life,” – riiight. So life first evolved at a time when conditions were hostile to it.
Strativarius’ comment here “the more complex the matter in hand – climate, genomes etc – the more certain they are that they and only they understand it” – is only half right. The other half is that the only thing that is certain about it all is that those experts don’t understand it.