In addition to them, 22 stemmed organisms of unknown nature were recorded.

Three "additional" positions (86, 88 and 101) were also usually pulled up to the state optimal for the given temperature conditions. All this happened many times independently in different evolutionary lines.

The authors even managed to figure out in general terms why the replacement of aspartic acid with serine in position 103 reduces the activity, but increases the stability of the enzyme. For high activity, the amino acid residue needs to form a strong hydrogen bond with the substrate. This is better for aspartic acid than for serine (Fig. 1, below). Stability requires that the amino acid residue be in the protonated state, that is, it ends with the -OH group, and not -O−. Aspartic acid has a problem with this (it’s still acid), but serine does not.

Thus, weak epistasis provides a simple and universal evolutionary route between KSI versions adapted to different temperatures. This, in turn, leads to numerous cases of parallel evolution.

To understand how common this pattern is, the authors analyzed data on 2194 enzyme families in 5852 bacterial species for which genomes and optimal temperatures are known. For each enzyme, each amino acid position in this enzyme, and each of the 20 amino acids that could in principle be in that position, the scientists looked for a relationship with temperature. In other words, a targeted search was carried out for positions in which the frequency of occurrence of certain amino acids reliably depends on temperature. If weak epistasis, the presence of standard evolutionary routes, and numerous parallelisms are general rules for temperature adaptation of enzymes, then one should expect that there will be a lot of such “temperature-dependent” positions and amino acids.

This expectation was confirmed. At least one temperature-dependent position was found in almost half of the enzymes (1005 out of 2194). Judging by the way the amino acids in these positions are distributed along the evolutionary tree, parallelisms in the evolution of these enzymes have occurred quite often.

The remaining 1189 enzymes apparently did not find universal (that is, not subject to epistasis) ways of temperature adaptation. They probably do it in other ways, not so universal, but only suitable for certain amino acid contexts. But this study is not about them.

In total, the researchers found more than 158,000 statistically significant associations between temperature and a specific amino acid at a specific position of a specific enzyme. One example is shown in Fig. 3.

Fig. 3. An example of a standard evolutionary route for temperature adaptation: position 452 of the enzyme phosphate acetyltransferase (PAT). The enzyme functions as a homodimer, that is, a complex of two identical protein molecules. Its structure is shown on the left. The amino acid at position 452 is involved in joining the halves. The graphs show that as the optimal growth temperature (TGrowth) increases, the likelihood that threonine (T) or asparagine (N) will be found in a given position decreases, and the likelihood that isoleucine (I) will be there increases. The evolutionary tree (on the right) shows that different amino acids in position 452 (colored dots at the ends of branches) are distributed throughout the tree, although not entirely chaotically, but without strict confinement of certain amino acids to certain branches. This means that there were many parallelisms in the evolution of this enzyme. Image from the discussed article in Science

As a result, an impressive array of data was obtained on the standard (highly probable) pathways for temperature adaptation of enzymes. It will be possible to search for all sorts of interesting patterns in this array for a long time to come. Some of them have already been found by the authors and are described in the article under discussion. Here’s one example. The idea has already been put forward that the evolution of thermal stability of proteins may be accompanied by an increase in the frequency of occurrence of branched-chain amino acid residues (isoleucine, leucine, and valine) in the hydrophobic core of the protein molecule. Branched chains hold it together like glue. The new data showed that the frequency of isoleucine does increase with increasing temperature, but for leucine and valine, such a pattern was not found. Apparently, this means that isoleucine is a more versatile (context-independent) adhesive than leucine and valine. Moreover, it turned out that the two most frequent amino acid substitutions that occur during the adaptation of enzymes to high temperatures are replacements of leucine and valine with isoleucine. The authors suggest that isoleucine adheres to a protein molecule better than valine, since it has a longer hydrophobic side chain, and better than leucine, because this chain is asymmetric, it can rotate in different ways and is easier to integrate into various voids in the inner part. protein molecule.

The standard ways of temperature adaptation of enzymes discovered by the authors are sometimes single amino acid substitutions, but in many cases we are talking about a coordinated substitution of two or more amino acids. This should more often happen with amino acids that somehow interact with each other, which means that they should be adjacent to each other in a three-dimensional protein molecule (approximately like positions 103, 86, and 101 in the KSI enzyme, see Fig. 1). A targeted search for such contacting and at the same time consistently changing groups of amino acids made it possible to find them in more than half (525 out of 1005) of enzymes that have at least one temperature-dependent position. In most cases, these are pairs, but there are also triplets and more numerous groups of interacting amino acids that tend to change consistently during temperature adaptation.

The discussed work has both theoretical and practical significance. A database compiled by the authors on amino acid substitutions associated with temperature adaptation will be useful in the design of artificial proteins with desired properties. From a theoretical point of view, it is important to conclude that temperature adaptation often (though not always) follows standard, highly probable evolutionary routes, the universality of which is ensured by weak epistasis. This leads to countless parallelisms: the most different versions of the enzyme, even very different from each other in amino acid sequence, over and over again find the same simple solution to a typical evolutionary problem.

Source: Margaux M. Pinney, Daniel A. Mokhtari, Eyal Akiva, Filip Yabukarski, David M. Sanchez, Ruibin Liang, Tzanko Doukov, Todd J. Martinez, Patricia C. Babbitt, Daniel Herschlag. Parallel molecular mechanisms for enzyme temperature adaptation // Science. 2021. DOI: 10.1126 / science.aay2784.

See also the role of epistasis in protein evolution:1) "Alternative history" of proteins sheds light on the role of randomness in evolution, "Elements", 09/18/2017.2) The evolution of proteins is constrained by the low permeability of the fitness landscape, "Elements", 09.02.2015.3) A predictable increase in fitness is achieved in unpredictable ways, "Elements", 06/30/2014.4) Parallel evolution studied in an experiment on bacteria, "Elements", 01.02.2012.5) In a long-term evolutionary experiment, selection for “evolutionary prospects” was revealed, “Elements”, 03/25/2011.6) The expansion of the protein universe continues, "Elements", 24.05.2010.7) The paths of evolution are predetermined at the molecular level, "Elements", 12.04.2006.

Alexander Markov

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Antarctic ice shelves (shown in blue). The circles mark the locations of the glacier drilling and its results: multicellular life forms were found in the wells depicted by black circles, multicellular life was not found in the wells depicted by white circles 1894 george orwell. An asterisk indicates a well in the Filchner Ice Shelf, from which new data on bottom ice inhabitants were obtained. Drawing from a discussed article in Frontiers in Marine Science

During an expedition to the Antarctic Weddell Sea, scientists examined the seabed under the Filchner Ice Shelf. To their surprise, a video camera, lowered into a hole drilled through the ice at a distance of 260 km from the edge of the glacier, filmed a separately lying boulder covered with biofouling: in the video, we could see several types of sponges (ordinary and on long stalks), as well as other stalked and filamentous organisms, both small and large. Scientists emphasize that it is the first time that attached benthic forms of life have been recorded at such a distance from the edge of the glacier. This means that there is enough organic matter in one form or another to feed multicellular animals and maintain the fouling complex. It was believed that at great aphotic depths under the ice, under conditions of an insignificant input of organic matter from the ice edge, the bottom life should come to naught. Past research, coupled with an exceptional paucity of data, has supported this hypothesis. However, the matter, apparently, is not so much in the low content of organic matter, as in the absence of convenient places for settlement.

A new publication in Frontiers in Marine Science, authored by an international team led by Cambridge polar biologist Huw Griffiths of the British Antarctic Survey, introduces the unexpected find of an Antarctic expedition. This expedition explored the sub-ice shelf of the Weddell Sea, including several wells drilled for various sub-ice surveys and soil sampling. The soil under the ice is usually represented by soft silts: this was known earlier and was once again confirmed during this expedition. But in one of the wells, the camera landed directly on a large boulder lying in the middle of endless silt (see video from additional materials). The entire article is devoted to the description of this boulder, and further reasoning of specialists is also based on it.

The boulder is located at a distance of about 270 km from the outer (oceanic) edge of the glacier. To get to it, it was necessary to drill 872 meters of ice and descend another 472 meters down to the bottom of the Weddell Sea. Complete darkness reigns there, and the water has a salinity close to the average for the World Ocean (34.61 ‰), and a minus temperature (−2.2 ° C). A fairly strong current was recorded, directed from the mainland to the edge of the ice cover, and not vice versa. And in these conditions, as you can see in the video, life flourishes on the boulder. The population of the stone has 38 relatively large animals and countless centimeter-sized small items. And around on the muddy bottom is empty: no worms, no crustaceans, not even traces of crawling.

Among the population of the boulder, first of all, sponges are noticeable. One sponge on a stem, its total length is about 40 cm. This is most likely a representative of predatory sponges.

Readers not familiar with predatory sponges may be interested in these photos. They show representatives of the Cladorhizidae sponges, a monophyletic family of about 150 deep-sea species. These sponges cling to the victim with hook-shaped spicules, they also secrete sticky substances on the surface of the epidermis or form sticky outgrowths to which small invertebrates adhere. Amoebocytes migrate to the contact zone, which surround the caught prey and digest it for several days. On the left is the thin-stemmed sponge Asbestopluma furcate (photo from the article by J. T. Hestetun et al., 2017. A review of carnivorous sponges (Porifera: Cladorhizidae) from the Boreal North Atlantic and Arctic), on the right is a beautiful sponge lampada (Chondrocladia lampadiglobus) with luminous spherical cavities (photo from pinterest.ru)

Already on this stone, 15 specimens of indisputable sponges without a stalk were noted, the taxonomic affiliation of which is not yet clear. In addition to them, 22 stemmed organisms of unknown nature were recorded. It can be stalked predatory sponges, and polychaetes, and hydroids, and ascidians … (experts in this place give an extensive list of types of marine invertebrates, demonstrating excellent zoological education). Some other incomprehensible attached thin threads were found, the length of which is about 1 cm. Besides the length, nothing more can be said about them.

It should be noted that at the second point of drilling, at some distance from the place of the first run, the camera removed a small rock placer. There were also some kind of attached organisms on these stones, but we could not really see them.

Photo of the lateral surface of the boulder with the outline of attached organisms: a predatory sponge is outlined in red, unknown stem-like organisms are in orange, and stemless sponges are in white. On the right, a filamentous organism is seen with an increase in the leader. Drawing from a discussed article in Frontiers in Marine Science

The authors of the discussed article were lucky for the first time to describe the benthic attached animals of the subglacial world of the deep waters of Antarctica. Prior to this, under the ice at long distances from the ice edge (more than 200 km), various nekton were recorded: mainly fish and crustaceans, but jellyfish, ctenophores, and chaetomaxis were also found. Not so long ago, on the ice shelf of the Ross Sea, 300 km from the ice edge, fauna was found in soft silts: there were ophiuras and some burrowing animals (unfortunately, I could not find any clarifications in the literature; see C. Stevens et al. ., 2020. Ocean mixing and heat transport processes observed under the Ross Ice Shelf control its basal melting). And now we see sedentary fauna. It includes predatory animals such as the Cladorhizidae sponges, as well as possibly seston feeders and filter feeders.

Aggregate data from all available observations of life under the ice on the Antarctic shelf. The horizontal axis shows the observation points with the mileage from the ice edge. At a distance of up to 200 km, cameras recorded both actively swimming (nekton, mobile) and attached (sessile) animals, and at a distance of more than 200 km earlier, only nekton forms were found. At the new observation points FSW1 and FSW2, 260 km from the ice edge, scientists recorded only sedentary life forms. Drawing from a discussed article in Frontiers in Marine Science

Now about the colossal under-ice areas of the seabed, one cannot say that they are lifeless. "Macro-life" is present in the depths under the ice, where only there is a suitable place for settlement and a source of food for it. In these areas, boulders and stones that have fallen to the bottom from melted floating ice (the so-called dropstones) turn out to be an excellent substrate for the formation of local biocenoses.

As for the power supplies, this question is still open. However, you need to understand that if fish, crustaceans and other animals live under the ice, far from the bright border of the ice edge, then they find some food for themselves, otherwise there would be no need for them to swim so far. The same can be said about the other settlers in these places. In theory, the farther from the edge of the ice, the poorer life is. Indeed, if there is no primary production of photosynthetics and the input of organic matter from the edge of the glacier disappears, then consumers of any order find themselves without food. But, apparently, some source of organic matter still remains, so it’s only a matter of a convenient place for life.