Origin of life

Summary

The question of the origin of life involving the storage of biochemical information represents a problem that, despite a wide range of approaches in the natural sciences, has so far remained unresolved. One reason may be that the environmental conditions required for this process have not yet been correctly identified. From a geological perspective, the protected environment of the continental crust offers ideal conditions. Within this setting, entirely new possibilities arise for identifying processes that may have been decisive for the emergence of the first cell.

Against this background, a theory was developed proposing that cellular life began with a pressure-controlled cycle at the interface of supercritical gases. The associated storage of peptide sequences in RNA occurred at crustal depths of approximately 400 to 1,000 meters within cavities of varying size. This cycle could operate within an open system linked to gas-permeable tectonic fracture zones containing high proportions of CO₂ and N₂ derived from the Earth’s mantle. The formation of peptides and vesicles in supercritical CO₂/N₂, as well as the chemical evolution of peptides, has already been demonstrated for the upper continental crust.

Further considerations address the interactions of vesicles with catalytic peptides and the formation of a proto-tRNA. Hydrophobic amino acids accumulate within the vesicle membrane, with their position in the membrane depending on their degree of hydrophobicity. With adenine at the tip of the acceptor arm of the proto-tRNA, membrane penetration becomes possible, allowing linkage to an amino acid upon contact. The depth of penetration is controlled by the hydrophobicity of the opposing anticodon. Separation of proto-tRNAs into single strands generates templates that enable the linkage of amino acids into short peptides. Upon vesicle disintegration during each cycle, the reaction products are released back into the cavities, where they accumulate. As a result, with each new cycle the vesicles take up an increasingly complex molecular mixture. At a certain point, the molecular composition reached the threshold required for the autonomous development of the first cell.

This immediately raises the question of why ribose, a five-carbon sugar (a pentose), forms the backbone of RNA, rather than one of the other pentoses or even the hexoses, which are six-carbon sugars. In laboratory experiments, such alternative nucleotide chains can indeed be synthesized. The various sugars must ultimately have been present in large diversity within the environments considered here, since their formation is not selective for a single type. On this basis, there were presumably a number of other RNA strand types that incorporated different sugars, which were likewise chiral and therefore existed in two distinct handednesses.

Which selection processes, then, could have led to the choice of ribose? Stability criteria or simple abundance—arising from the separation processes described above—certainly must be considered. However, another cause may have been decisive, arising from the tight loop of the proto-tRNA strand described above. The three bases that are forced to point outward for steric reasons must, in combination with the sugar molecules, have been arranged such that they could be read as a single unit, as a triplet block. Any alternative configuration that did not ensure this property would not have allowed further evolutionary progress.

It therefore becomes necessary to compare whether alternative sugars—both other pentoses and hexoses, as well as others—can yield an RNA loop configuration that includes an outward-facing, “readable” triplet block. Any arrangement of bases that impairs or prevents such readability would not be selected, because no information supporting enzymatically assisted catalysis could be retained in subsequent development. If this line of reasoning holds, ribose would have been selected from the multitude of sugars purely for steric reasons, that is, because it is structurally best suited to form an anticodon in combination with bases and phosphate.

It is striking that all tRNAs that are specifically charged with an amino acid today always possess the same base sequence CCA at the acceptor stem (Fig. 7). This binding sequence must have proven so successful in the earliest phase that it has been used exclusively up to the present day. The synthetases—today’s complex enzymes that carry out the specific charging of the corresponding tRNAs—recognize the now more complex tRNAs via their additional loops and the specific bases contained therein, thereby ensuring the critically important accurate assignment of the amino acid to be linked. The question remains why the version with the CCA acceptor arm emerged as the apparently sole representative from the group of medium-length RNAs through the selection process.

The cause may lie in an advantage conferred by a specific property of the proto-tRNA. In principle, any amino acid could have been attached to any proto-tRNA. Where, then, did the possibility for a specific assignment arise that is necessary for the establishment of an information storage system? Present-day conditions at least allow a coarse distinction. There are two classes of synthetases that perform the specific charging of tRNAs. Class I synthetases catalyze the attachment of hydrophobic amino acids at the 2′-OH group of the terminal ribose (Fig. 8), whereas class II synthetases catalyze the attachment of hydrophilic amino acids at the 3′-OH group [13].

However, given the seemingly infinite number of possible combinations in peptide formation, no repetition of the same sequences in the amino acid chains can be expected. What is missing is a storage of the information about the sequence, as it can be found in the later formed RNA or DNA.

However, the importance of vesicle formation is reflected in several properties that have played an important role in the development of life.

- On the one hand, it becomes clear how easily vesicles can be formed as precursors of cell compartments.

- On the other hand, an interaction between the membrane and molecules occurs, which can lead to special reactions and chemical evolution.

- Furthermore, the type of vesicle formation is suitable for taking up large molecular complexes that are formed in the free environment of the cavities during droplet formation.

The Hypothetical Model for Information Storage

For the storage of information on amino acid sequences in peptides, a mediating molecule must have been required that corresponded to a simple version of a tRNA (see above). This proto-tRNA is assumed in the model presented here for the development of the first cell. The use of DNA as the carrier of genetic information is assumed to have occurred at a later stage, since its stability under the conditions of hydrothermal disturbance zones would not have been sufficient.

The Onset of Information Storage

The formation of vesicles under pressure and temperature conditions corresponding to depths of approximately 1,000 m within the continental crust of the young Earth (see above) has been demonstrated repeatedly in laboratory experiments [2, 4]. Up to twelve amino acids can be formed under hydrothermal conditions in the crust [15, 16], with their relative abundances depending on the specific formation conditions. The hydrophobic amino acids isoleucine, valine, leucine, and phenylalanine—known to be formable under hydrothermal conditions—could theoretically be incorporated into membranes during vesicle formation, although energetic barriers exist. This limitation does not apply when several identical or similar amino acids associate to form short peptides; in this form, incorporation into the membrane becomes readily possible. The hydrophilic amino acids threonine, serine, proline, glutamic acid, aspartic acid, and lysine remain in the aqueous phase of the droplets unless they are incorporated into peptides predominantly composed of hydrophobic amino acids. Glycine, as the only non-chiral amino acid, represents a special case and can occupy different positions.

The vesicles consist of distilled water containing a fraction of organic molecules. Differences in salt concentration between the interior and exterior lead to instability, resulting in rapid destruction during the subsequent geyser eruption. The same vesicle-formation process occurs with water droplets that are hurled from depth above the water surface of the cavity during a turbulent geyser eruption. The vesicles formed in this manner are significantly larger, contain much higher concentrations of organic molecules, and exhibit the same salt concentrations as the surrounding water. As a result, they are more stable than vesicles derived from mist droplets and provide higher concentrations of organic molecules for chemical reactions.

Hydrophobicity as a controlling factor

In the simple proto-tRNA outlined above (Fig. 7), the adenine base is positioned precisely at the tip of the strand that is unpaired in this model, owing to the base sequence ACC. The acceptor arm can penetrate the membrane due to the hydrophobicity of adenine, thereby coming into contact with hydrophobic amino acids (Fig. 11). Under these conditions, linkage at the 2′-OH position of the terminal ribose becomes possible within the geyser cycle.

Fig. 11  Variation in Penetration Depths of the Acceptor Arm into the Membrane Depending on the Hydrophobicity of the Anticodon

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

The ACC arm

From a mechanical perspective, fixing a finger in a plastic medium is more favorable when the tip is thickened (comparable to inserting a lollipop into firm pudding). With the base combination “ACC” in the acceptor arm, adenine—with its two ring structures (purine scaffold)—is followed by two smaller bases, cytosine, each with a single ring structure (pyrimidine scaffold). This combination likely proved to be the most favorable (Fig. 12).

In the chemical evolution leading to the “ACC” arm, numerous variants must have arisen that were unsuitable or less suitable due to molecular size and/or degree of hydrophobicity (Fig. 13).

With guanine at the tip, a hydrophilic base is present that blocks penetration into the membrane, irrespective of which nucleobases follow. With adenine at the tip and the smaller pyrimidine base uracil, penetration of the acceptor arm into the membrane is possible; however, uracil is more hydrophilic than cytosine, making the combination with cytosine more favorable. If adenine is present not only at the tip but also at additional positions, fixation within the membrane becomes too strong, such that fine control of the penetration depth by the anticodon is no longer possible.

Wobble pairing

A particular feature relevant to the specificity of the genetic code is the variability of the third base of the mRNA codon (5′→3′) or, correspondingly, of the anticodon (3′→5′). In triplets encoding the same amino acid, there is often only variation in the third base (wobble pairing). Consequently, the contribution of the third base to specificity is lower than that of the first and second bases. It is worth considering whether a connection to the hydrophobic/entropic effect may have existed. For example, if the forces acting on a membrane-coupled proto-tRNA are considered in terms of force vectors (Fig. 14), the influence of the first two bases on the direction of penetration of the acceptor arm—due to molecular configuration—is greater than that of the third base.

Fig. 14 Direction of the force vectors of the hydrophobic/entropic effect as a function of molecular structure.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

The proposed model of positioning the tip of a single-stranded proto-tRNA within a membrane requires a strict correlation between the hydrophobicities of the amino acids and those of the nucleobases or anticodons. Table 1 shows, when comparing anticodon assignments with their corresponding amino acids, that all hydrothermally formable hydrophobic amino acids possess an adenine in the central position and/or additional adenines at the periphery (right). Hydrophilic amino acids exhibit the opposite pattern. Weber and Lacey [17] already identified this striking correlation in 1978, although they were unable to provide an explanation. This relationship becomes particularly evident in the table compiled by Jungck (1978) when only hydrothermal amino acids are considered (colored fields, excluding codons at stop positions).

The different proto-tRNAs could thus be linked to amino acids in a relatively specific manner via the hydrophobicity of the anticodon. At the same time, the single double-stranded region of the tRNAs could be readily separated, yielding a single strand. In this context, adenine–uracil (A–U) base pairing is less stable than guanine–cytosine (G–C) pairing, which involves one additional hydrogen bond. The resulting single strand constituted an information strand that initially had no functional meaning due to its random nucleotide sequence. Because charged tRNAs were present simultaneously, and those stabilized by G–C base pairing remained intact longer upon temperature increase than proto-tRNAs with A–U pairing, they could use the “A–U” strand as a proto-mRNA and form a tetrapeptide, provided suitable conditions were present.

Some of the “tRNA templates” could not be used to produce a peptide because they provided positions for amino acids that did not yet exist. This also applies to the complementary strands generated during replication, which is regarded as a prerequisite for the survival of proto-tRNAs (Fig. 16). After replication, for example, the CCA segment in the complementary strand corresponds to the amino acid tryptophan, which was presumably not formed hydrothermally and only later occupied the UGG codon. By analogy, UGG may originally have encoded threonine.

Because proto-tRNAs had to exist in homochiral form (both D and L versions) in order to be formed as such, and because there is a preferential linkage of L-amino acids to D-RNAs (and vice versa) [23], the resulting peptides were also homochiral (present in equal amounts of both chiralities). Since at most twelve different amino acids could have been present with different proto-tRNAs—some of which may have existed in multiple forms for a given amino acid—a large variety of templates for tetrapeptides was available. The linkage of two tetrapeptides of the same chirality yielded lengths comparable to membrane thickness. This already allowed the formation of pores required for concentration equilibration. Because the peptide sequences were already stored, only the combination of tetrapeptide chains or of the corresponding complementary RNA strands was required to obtain the first functional molecules with catalytic activity. If these contributed to faster formation of additional functional and other “useful” molecules, they would win the competition for resources and establish their chirality.

If this process for the first time involved a molecule with catalytic function that was subsequently retained, for example as the core of more complex peptides, this point may be regarded as the origin of life.

Advantage of using the opened proto-tRNA as a template:

If both the single strands of the tRNA (provided the codes correspond to hydrothermal amino acids) and, simultaneously, the complementary strands are used as templates (Fig. 16), catalytically active peptides can be generated that later, in DNA, exhibit bidirectional genetic encoding (sense/antisense orientation).

Fig. 16 Proto-tRNA as a single strand that can function as a template. An additional template is provided by the complementary strand. Tetramers can be formed from both, which are homochiral due to the tRNA. However, single-strand formation involving A–U base pairs was more readily achieved upon temperature increase, such that charged tRNAs with G–C pairing could already utilize these strands as templates.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

As mentioned above, there are two classes of synthetases responsible for the specific loading of tRNAs. Amino acids associated with Class I synthetases, which are linked to the 2'-OH end of the terminal ribose, are generally larger and less polar, while those associated with Class II synthetases, which are attached to the 3'-OH end, are smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that these two classes originate from opposite strands of the same ancestral gene [25]. This would support the idea that the basis for the evolution of today's aminoacyl-tRNA synthetases dates back to a very early phase, which is related to the template formation described above.

Table 2: Complementary groups of amino acids that can exhibit a relationship in the use of templates from proto-tRNAs and their complementary strands.

ATP

Of particular interest is the formation of ATP (adenosine triphosphate), which is the principal energy carrier in modern cells. ATP is produced by a complex process that evolved only gradually over evolutionary time. For many reactions at the onset of life, ATP would have been an attractive energy source. As shown above, the vesicle membrane can act as a catalyst. If proto-tRNA with adenine at its tip is able to penetrate the membrane, this must also have been possible for AMP (adenosine monophosphate) (Fig 17). Assuming that the required molecules were present, the formation of ATP can therefore be postulated. Corresponding experimental approaches appear conceivable.

Consequences

From the relationships discussed above, the following assumption can be made: both the single strands of the proto-tRNA consisting of twelve nucleobases and, simultaneously, their complementary strands could be used as templates from which catalytically active peptides were formed.

The four triplets of each possible proto-tRNA (there were more than 65,000 possible variations; the same number of tRNAs with opposite chirality is not discussed here) initially lacked the informational content required for a functional molecule. They represented random combinations from which tetramers could arise. A prerequisite, however, was that suitable tRNAs and corresponding amino acids were available for the respective triplets, since not all amino acids were present in this environment at the beginning. If such an RNA was copied repeatedly, the information about the sequence of the corresponding tetramers was also retained.

And chirality?

The development of chemical evolution toward D-ribose in RNA and L-amino acids in peptides might possibly be explained by a случайный (random) excess of one enantiomer at a particular point in time, although this is difficult to reconstruct. In principle, equal amounts of D- and L-molecules always exist, such that all reaction steps in the initial phase must have occurred with both. This would have remained the case until the point at which the first catalytically active peptide emerged that was stored in RNA and decisively shaped further development (the start of life). This peptide ensured that, through faster formation of successor molecules, resources were increasingly consumed by this group (today’s D-ribose and L-amino acids) [18, 19]. The probability that such a peptide arose at exactly the same time in both the D- and L-forms is vanishingly small.

A three-way relationship: membrane, peptide, and RNA — the MPR world

From the preceding considerations, it becomes clear that there was no isolated “RNA-first,” “peptide-first,” or “metabolism-first” world, as described above. Rather, three players must have coexisted simultaneously, undergoing chemical evolution in mutual interdependence: the vesicle membranes, which enabled separation of hydrophobic and hydrophilic amino acids; peptides, which initially formed unspecifically and later in an information-driven manner; and an RNA composed of the minimal possible number of nucleotides. In abbreviated form, this can be termed the MPR world.

Whereas some other models require information for enzyme formation to be present at the very beginning, the model presented here proposes that an unspecific sequence of codes arose first, which could be coupled to a sequence of amino acids in peptides. Only after a proto-enzyme crystallized out of random combinations from the pool of many unspecific codes—one that possessed properties supportive of further cellular development—was the information fixed as such in the RNA, which thereby became established as a proto-mRNA. Accordingly, it was passed on to subsequent generations by copying of the proto-mRNA. Only through validation by selection did the segment stored in RNA, and later in DNA, acquire its functional significance. 

An interesting consideration arising from these ideas concerns the further evolution of enzyme formation, by which the rate of emergence of the first cells was determined.

What situation is conceivable? It is possible that a larger number of 12-nucleotide modules were linked to form a longer proto-mRNA strand (Fig. 18-1). Provided that specifically charged proto-tRNAs occupied appropriate positions and the transported amino acids could be linked into a chain, it was only a matter of time before certain combinations yielded catalytically active peptides (proto-enzymes).

It must be taken into account, however, that only parts of the proto-mRNA were occupied at any given time, since suitable tRNAs and amino acids did not yet exist for all triplets and/or sufficient building blocks were not available. Some of today’s canonical amino acids appeared only later in evolution.

One may envision the situation as analogous to a toothed belt strand from which many teeth are missing. Longer complete sections are bounded by gaps. For mRNA, the longer sections would correspond to regions from which a continuous amino acid chain could be formed. The delimiting gaps would thus have assumed the function of start and stop triplets that later became necessary for the decoding process.

And now it becomes particularly interesting: If, due to external influences or to enzymes that had meanwhile become active, a new amino acid with its corresponding tRNA (of which sufficient variants existed; see above) appeared in the system, the matching triplets of the mRNA that had previously remained unoccupied could suddenly be filled. This occurred not at a single site, but distributed across the entire strand wherever the corresponding codon was present. In the most favorable case, a gap between two peptide complexes was closed, and together they suddenly acquired higher functionality than either alone. This offered the opportunity to generate new large peptides/enzymes within a very short time, which represented more effective catalysts than the smaller precursor peptides on their own. In evolutionary terms, this could have resulted in major leaps forward each time. In contrast to a mutation that acts only locally, perhaps in a single individual, this change affected many positions within the information store and could thus occur simultaneously in all RNAs present in the environment.

This concept can also be applied to later stages of life’s evolution. Non-coding regions of DNA (so-called junk DNA) provide numerous points of departure for the establishment of new enzymes. Whenever major upheavals occurred in the Earth system, rapid adaptations of the biosphere to new environmental conditions followed. A particularly significant event in Earth’s history was, for example, the appearance of oxygen in the atmosphere. Oxygen can, for instance, convert the nucleobase guanine into 8-oxo-guanine, which can mispair with adenine instead of cytosine. It is unclear whether this specific effect occurred; it merely serves to illustrate that, through an environmentally driven influence affecting all or most organisms, even minimal changes in a single DNA component can rapidly lead to pronounced alterations in the blueprints of enzymes and other biomolecules.

Fig. 18-1

Fig. 18-2

The Keystone

It has become clear that there was an interplay between vesicle formation and processes occurring within the cavities of continental fracture zones. Within these cavities, organic molecules initially accumulated, including building blocks required for the formation of the first cells. Through vesicle formation, these building blocks (amino acids, nucleobases, lipids, among others) were taken up, enabling them to react with one another within the vesicle interior [28].

The vesicles can be regarded as the production sites of enzymes whose information was stored in RNAs. Upon subsequent disintegration of the vesicles, these molecules were released back into the cavities, making them available again for the next cycle. It is readily apparent that the lifetime of vesicles—on the order of only a few tens of minutes—was insufficient for the development of complex molecules. Even the formation of uncoded peptides, which were newly generated with random sequences in each cycle and could assemble into membrane pores, extended vesicle lifetimes only marginally.

However, through the release of coded peptides upon vesicle breakdown, a wide variety of enzymes accumulated in the cavities over extended periods. Although flows and turbulence existed within the water-filled fracture zones, sufficient protected regions were present in which accumulation could occur. Over time, an increasing number of functional molecules thus became available and could be taken up into vesicles with each new cycle. In their presence, additional and more complex reactions became possible. At the end of each cycle, however, all components were again transferred back into the cavities. In this state, the cavities corresponded to oversized cells (“giga-cells”), albeit without a surrounding membrane.

While storage of information within vesicles was more favorable, RNA could more readily be copied within the cavities (Fig. 19). The high concentration of enzymes present there, together with the simultaneous existence of RNA strands, provided ideal conditions for the development of more complex molecules, such as the ribosome or DNA. The lifetime of this environment was on the order of millions of years.

This means that the cavities functioned simultaneously as reaction vessels and as storage sites for the building blocks of life. With each vesicle formation event, material could be drawn from the reservoir of the giga-cell, such that it was only a matter of time before a favorable mixture of functional molecules was taken up into one or more vesicles, enabling the transition to autonomous replication (Fig. 20) [29].

Fig. 20 The decisive moment of optimal loading of a vesicle with functional molecules, followed by autonomous replication and physical division through shear forces.

Mirrkaryotes 29.09.2025

The previously outlined possible path to the first cell diverges at a certain point, separating the parallel development of the handedness of L-amino acids and D-ribose in the RNA of the present-day world from the alternative path involving D-amino acids and L-ribose. The question arises as to whether the development proceeded uniformly at all the numerous potential locations, or whether, after the initial expansion of the first cells from a singular origin, local conditions in other regions were so significantly altered that they led to a convergent outcome. The latter scenario appears to be the most plausible.

However, there is likely some chance that at a different site, perhaps on another small continent, a similar evolutionary path to the first cell occurred, but one that led to the opposite, mirror-image system. This would represent, alongside the life form LF1 as we currently know it, a second form, LF2. While LF1 is divided into the domains of Bacteria and Archaea (both prokaryotes), as well as Eukaryotes, LF2 could have consisted of only a single domain. The term Mirrkaryotes would be fitting for such a system.

In this context, the immediate question arises as to whether these "Mirrkaryotes" might still exist today, in inaccessible areas such as the deep biosphere, perhaps in the oldest continental cores. This leads to the crucial follow-up question: Would we be able to detect them with our current analytical methods and distinguish them from other single-celled organisms? It is possible that they have always existed alongside us, without our having taken notice of them.

What happened next?



The geyser eruptions continuously carried organic molecules and eventually the first self-replicating cells to the surface. Consequently, "bio-films" made of organic materials must have formed in the vicinity of the exit points, in which the first cells were also embedded. However, they had little chance of surviving under the new environmental conditions. UV exposure, solar wind, lower temperatures and higher pH levels required an adaptation that took a longer period of time.

In addition, the energy and substance supply was difficult. However, the biofilm in the vicinity of the geyser probably provided the conditions for the cells to be able to absorb substances from outside. Sooner or later, climatic or regional conditions may have made it possible for the cells to survive on the earth's surface, so that they could reach the oceans via rivers. An alternative situation is conceivable for locations close to the coast, whose open fault systems lead directly into the marine environment. Entering the ocean was the decisive step that set the system of life in motion. In the ocean, the cells encountered areas that were familiar to them in terms of physicochemical conditions. It was the Black Smokers and other hydrothermal vents that provided them with unlimited, usable energy resources. At the same time, this environment again offered protection from the destructive influences that were present on the surface of the earth.

The appropriation of the submarine hydrothermal vents by the first prokaryotic cells probably led to an explosive spread of the first life form, viewed in a compressed time period. The open ocean offered ideal conditions for this with sea currents and a sufficient number of hot springs.

Long distances and unique local characteristics could lead to independent adaptations in the young family of cells, which quickly diversified as a result. This phase marked the end of the violent meteorite impacts, which mainly affected the oceans. Every major impact caused large areas of the young continents to be flooded. This was the way in which the prokaryotes were able to spread over all the large and small fragments of continental crust that had now been formed. Wherever they came into contact with hydrothermal vents on land, they could gain a foothold and continue developing.

In this context, another development on the young Earth is significant. The movement of plates began early on, which ultimately led to the shifting of the continents and subsequent collisions. What influence did this process have on the further development of the prokaryote?

The contact between differently developed cells

It is now accepted that organelles such as the mitochondria and chloroplasts of eukaryotes are derived from bacteria. There is an idea that bacteria were taken up by other prokaryotes but could not be digested. On the contrary, the absorbed bacteria continued to live in the host's cell envelope and used their metabolic products for their own sustenance. An endosymbiosis developed in which one partner lives permanently in the body of the other, like the bacteria in the intestine. The evolutionary adaptation meant that the "undigested" bacteria were gradually reduced to useful building blocks that today make a decisive contribution to the energy supply of the cell.

The eukaryotes appeared almost spontaneously on the stage of life 1.5 billion years ago. Ancestors that could be considered as transitional stages have not yet been clearly identified. 500 million years earlier, almost all existing small continents began to migrate towards one another, until a supercontinent had formed 300 million years later. It is referred to by geologists as Columbia. Its existence lasted for another 200 - 300 million years, whereby the last 100 million years were already characterized by decay and mountain building processes caused by plate tectonics. Finally, in the final phase of Columbia, the eukaryotes appeared. A billion years earlier, the concentration of oxygen in the atmosphere began to increase, to which the living world had to react.