Crafty ancestor: how all living things began

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Crafty ancestor: how all living things began
Crafty ancestor: how all living things began
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Man is not like an amoeba, but at the molecular level, we are made almost the same. What did our common great-great-grandfather look like? Nikolai Kukushkin - about what he was, where he lived and what the last common ancestor of all living things ate.

microscope

Outwardly, multicellular animals may have little in common with, say, molds. But if you look under an electron microscope, you will find that there is almost no difference between us. We are all made up of cells. All cells are surrounded by a lipid membrane. They are all served by proteins and RNA encoded in the DNA double helix. Finally, all living things get energy in the same way. All of these properties indicate that all life forms known to us had a common ancestor, also known as LUCA (last universal common ancestor).

Why is the ancestor common

Life, most likely, has arisen many times. Perhaps a million times. But only once the emerging life was so successful that it gave rise to all the diversity of living nature that we observe today. This isolated case is just LUCA.

The idea that all life comes from a single organism is usually attributed to Charles Darwin, who saw in it the logical conclusion of his theory of evolution. It is clear that neither Darwin nor anyone else has seen a common ancestor and is unlikely to ever see it - we are talking about a creature that vaguely resembles a bacterium and lived in an unknown place about 3.5 billion years ago.

Why, then, are we so sure that all living things had a common ancestor? Because all living things are very similar. In 2010, the American biochemist Douglas L. Theobald mathematically analyzed the sequences of several ubiquitous proteins. The selected molecules are present in humans, flies, plants, and bacteria - but could they have appeared independently? Theobald calculated that a common ancestor was not just more likely, but at 102860 times more likely. The number of atoms in the universe, for comparison, is 1080.

Common ancestor research is usually organized along the same lines: we compare ourselves with everyone else (bacteria, archaea, plants) and try to understand which elements of our device are universal and, therefore, have a common origin.

For example, almost all scientists are convinced that LUCA was a cell. First, we simply don't know life without cells today. Secondly, it is very difficult to imagine it. Life began in the ocean. The ocean is an incredibly large body of water. No matter how many active, "viable" molecules appear in it, their concentration in the ocean will be virtually zero. In order for these molecules to begin to react productively with each other, they must be placed in an enclosed space - for example, a cell surrounded by a lipid membrane or membrane. The membrane is considered one of the fundamental properties of living things - and therefore one of the distinguishing features of our common ancestor.

In addition to the membrane, life requires molecules that can reproduce - either by themselves or with the help of other molecules. Today the most famous such molecule is DNA. But the first self-replicating, "living" molecules from which LUCA ultimately originated were RNA. Some scientists even suggest that LUCA did not have DNA at all - it independently appeared in his descendants. One way or another, the common ancestor definitely had a self-replicating genome - from DNA or RNA.

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Finally, food is essential for life. Only by consuming energy can we create a more ordered system from a less ordered system, that is, having less entropy.What did the last common ancestor of the living eat?

RNA - the molecule of life

How do we know that life began with RNA?

First, RNAs code for proteins - the backbone of modern cells - but not vice versa. Moreover, the ribosome - a molecular machine that "decodes" RNA into protein - consists mainly of a special type of RNA. That is, RNA is theoretically completely self-sufficient

Secondly, RNA can evolve - this has long been shown experimentally. The sequence of the RNA strand in the test tube will randomly change - if in this case, somehow “useful” changes are selected, a complete and observable evolution is obtained

Third, RNA, unlike DNA, is a fairly active molecule. It can catalyze reactions - almost like a protein that performs almost all functions in a modern cell. You can, for example, artificially create an RNA that will exactly copy itself without additional devices

Molecular Gasoline

Almost all the molecules that make up living things run on the same fuel: adenodine triphosphoric acid, or ATP. To exist, the cell - the most important universal unit of living things - needs to constantly produce this substance. This requires energy from the outside.

The energy source may vary. Plants absorb it from sunlight. Animals break down food - biofuel. Some bacteria are content with mineral fuel. But the final stage is always the production of ATP. And ATP is produced in all life forms known to us in the same way - with the help of a molecular turbine, spun (literally) by a stream of ions. Most often, a proton is used as the unwinding ion.

A proton, or hydrogen ion, is the simplest positively charged particle that, together with a negatively charged hydroxyl ion, makes up a water molecule. A small percentage of water molecules are in a split state all the time: the proton exists separately from the hydroxyl ions. There are as many protons in pure water as there are hydroxyls. With the addition of acid, there are more protons. Alkali, on the other hand, adds hydroxyls to the solution.

Imagine that there is a microscopic, but very intelligent creature sitting in the water column that can distinguish protons from hydroxyl ions. In physics, such hypothetical creatures are called demons - ours, for example, is very reminiscent of the famous demon Maxwell. This underwater demon grabs the protons and forces them into the bag. There are more protons in the bag than hydroxyls - water turns into acid. If now we make a hole in the bag the size of a proton, then they will burst out of the bag like a jet: from high concentration to low concentration. That is, the difference - or the gradient of the concentration of protons contains energy, just like the water that rotates the turbine of a hydroelectric power station.

Where did this energy come from?

In our example, the energy source is a demon making efforts to sort out protons and hydroxyls. Energy is stored in a bag and is released when a hole is made in it. If one contrives, then this energy can be collected - as a hydroelectric power station built on a river collects it - and do something useful with it. It was in this way that several billion years ago the ancestors of all living things learned to produce ATP: they invented a turbine, the rotation of which fed the synthesis of this energy molecule. But what, if not a magic demon, created the proton gradient necessary for the synthesis of ATP?

Which came first: a saucepan or a soup?

Modern organisms produce gradients themselves. This is always done according to the same scheme: protons are pumped somewhere (or pumped out from somewhere) by special protein pumps, which spend energy for this from food or, for example, sunlight. The pumps are embedded in a membrane impermeable to protons - because of this, they cannot simply leak back.As a result, on one side of the membrane there are a lot of protons, on the other - few, as in the example with the demon and the bag. The "proton lock" - the hole in the bag - opens, and the protons rush back to where there are few of them, spinning the turbine and producing ATP. In our country, this happens in mitochondria, in photosynthetic plants - in chloroplasts, in bacteria - on their own cell membrane. But the artificially created ion gradient itself is universal.

If something is universal, then, based on the theory of evolution, it is most likely that a common ancestor also had it. It is very difficult to assume that such similar systems of accumulation and production of energy independently appeared in all kingdoms of the living. LUCA had to use gradients with might and main even before he initiated the two main branches of evolution: archaea and bacteria.

But here a paradox arises, which for many years haunted evolutionists and biochemists.

Three domains

The most popular model of the division of the living world today was first proposed in 1977 by Carl Woese. Based on the analysis of ribosomal RNA genes, he concluded that all living things are subdivided into three kingdoms, or domains (the last term was introduced in the 1990s): bacteria, archaea and eukaryotes. Bacteria and archaea (also collectively referred to as "prokaryotes") are superficially similar - for example, neither have a nucleus. But at the same time, they differ greatly in the details of the molecular structure. In some ways, archaea are closer to eukaryotes, which include all organisms with a cell nucleus, including animals, plants, and fungi

In recent years, the classic "triple" evolutionary tree has begun to change. Most scientists today believe that eukaryotes evolved through the fusion of archaea and bacteria. In addition, it is not a fact that a clear tree of early evolution can, in principle, be built: most likely, there was a constant horizontal exchange of genes between early organisms, which blurs and complicates the concepts of a species and even a domain

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One of the main differences between modern bacteria and archaea is the structure of their membranes. In both kingdoms, or domains, cell membranes are composed of lipids, but chemically, these lipids are dramatically different. The proteins in the membranes are also completely different - only the rarest and most ancient molecules are similar, like the very "proton turbine" that everyone has. According to the logic of evolution, this should mean that the composition and structure of membranes in bacteria and archaea were formed after separation. And the gradients, as we found out, were even before the separation. But gradients need membranes and protein pumps! How could it happen that a common ancestor already “fed” on gradients, but did not yet know how to “cook” them?

The answer may be that proton gradients were not produced by ancient cells. Rather, they were assimilated from the external environment.

The acid river and the pump that changed everything

A group of British scientists led by Nick Lane offers the following explanation. According to the most common version, life originated in the depths of the ocean next to underwater hot springs. In such an environment, changes in proton concentrations can form naturally: an alkaline environment near sedimentary rocks produced by a hot spring smoothly transforms into a weakly acidic environment of the ocean. If you settle down exactly on the border of an acidic and alkaline environment, then this can be used. On the one hand, there will be more protons, on the other - less. Difference means "flow". Flow means energy. Lane and his colleagues believe that this is how our supposed ancestor first got the idea of ​​converting the concentration gradient into useful energy - an ATP-synthesizing turbine was built on the natural "river" of protons.

There are several consequences of this model. First, there is no need for pumps: the proton gradient is formed by itself due to the drop in acidity.Secondly, in order to take advantage of this gradient, the cell membrane must be easily permeable to protons - otherwise, the difference in their concentration will not affect it in any way. That is, the "bag" must be full of holes. Thirdly, the cell must be motionless: if it moves from a good "gradient" place, then there will be no gradient, and since the membrane is easily permeable, it will not work to "carry the gradient with itself" - the protons will simply move freely between the cell and the external environment …

How, then, did the ancestors of bacteria and archaea learn to live far from the life-saving hot springs? Lane and his colleagues believe that the emergence of the proton-sodium pump played a major role in this. It is a membrane protein that exchanges protons for an equal amount of sodium ions. That is, a “natural” proton gradient can be converted into an “artificial” sodium gradient using a sodium-proton pump. The advantage of this method is that it is much more difficult to push sodium through a "leaky" membrane than a proton. That is, the difference in sodium concentration is "preserved" better than the difference in proton concentration.

Pumps that artificially create a proton gradient could not appear on their own with a leaky membrane: they simply would not make sense. If the diaphragm is leaky, as Lane's group mathematical calculations show, the pumps offer no advantage. But if you add a "exchanger" - protons for sodium - the accumulation of gradients becomes much more efficient, and significant benefits appear in the pumps.

What happens next? The cell continues to evolve. Since the pumps are efficient, it means that gradually there will be more and more of them - as long as it is beneficial. Since there is a proton-sodium "exchanger", it means that everything accumulated can be carried with you. There is no need for a "natural" gradient: the cell becomes autonomous. At the same time, there is no need for a leaky membrane - on the contrary, a strong membrane retains gradients much better. As soon as the membrane becomes solid and no longer allows protons to pass through, there is no point in sitting in a hot spring.

In total, the proton-sodium "exchanger", according to Nick Lane, by its appearance caused a chain reaction of evolutionary transformations, as a result of which immobile, leaky half-cells, completely dependent on hot springs, turned into tight-fisted and sagacious explorers of the ocean depths - and ultimately into all the diversity of modern nature. It was after the emergence of the "exchanger", according to the researchers, that the separation of bacteria and archaea, the two main branches of early evolution, took place. Their membranes “hardened” in different ways - but both groups retained their fidelity to ion gradients as the final stage of energy processing.

The biology controversy of LUCA - the great-grandfather of all living things - is unlikely to ever be resolved by unambiguous data. Great-grandfather's body has decayed over billions of years - but his spirit lives on. Our body is still encoded in the nucleotide sequence. It is still made up of cells. We learned how to extract energy from sandwiches - but to absorb it, we still arrange an ancient hot spring in every cell.

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