venerdì 5 maggio 2017

The origin of life: The proto-organism

Post n.31 English

Research on the origin of life began only in the first half of the last century, after centuries of theological and philosophical discussions. Today, after more than half a century of research, scientists have only one certainty: life originated from inanimate matter.
We have dealt with all the issues that affect the origin of life in all articles published in the Blog. It is time to make a synthesis and try to figure out how life may have originated from inanimate matter. The statements and concepts of these articles on which the publish number will be placed in parentheses for those who want more clarification, will be mentioned briefly.
If the question is: how did life originate? We are beginning from life to understand how it may have originated.
We have defined the bacterial cell as the smallest vital entity, the first stage of life (post 30).
But all scientists agree that life cannot have started directly with the cell. Even bacterial cells in their simplicity, compared to the cells of higher organisms, are still of enormous complexity. It is therefore believed that between the chemical period, that is, the phase in which the fundamental substances of life accumulated and interacted, and the appearance of the cell, there was something intermediate that scientists call: proto-organism, or proto-cell or pre-cell phase. The term proto-organism used by Mario Ageno at the beginning of the 1980s is used here, and it seems to give the idea of ​​this intermediate stage better.
Now, the problem is that all scientists talk about proto-organism but nobody knows what it is.
So the problem is, first of all: to define the proto-organism, to understand how it may have originated from inanimate matter and then how it turned into cell.
Before we go ahead, some clarification is needed.
Firstly, for proto-organism, we don’t refer to a single and solitary entity that appeared on earth and from which only one cell emerged. With Proto-organism, we mean billions of billions of entities, chemically quite similar, spread across the surface of the planet. Perhaps for some researchers this is not so, anyway this is how we are considered in this discussion.
Secondly, the Proto-organism was a dynamic entity within which a chemical evolution took place, that is, processes that led billions of them to achieve the cellular state.
 Other proto-organisms, perhaps the majority, took the wrong path, they disappeared into the environment.
Finally, we do not know the processes within the proto-organism, we can only make hypotheses. In order to make some assumptions we must try to identify the chemical bases of the proto-organism, that are, the molecules that may have begun these processes.
Here is another problem, scientists not only do not have a definition of proto-organism, they do not agree on how to begin to define the proto-organism, that is identifying the chemical bases of the proto-organism.
In fact, for some scientists first compartments appeared lipid vesicles, liposome-like membranes, within proteins and nucleic acids accumulated, capable respectively of metabolism and replication. Pier Luigi Luisi is an authoritative exponent of “compartmentalists” and as he states in “Origine della vita e della biodiversità” 2013, proto-cell compartments are indispensable for
the origin of life.
 For many other scientists everything started through only metabolic processes within polymer membranes (first the metabolism), while for others it appeared only to replicate first molecules (before replication, RNA World).

But on these theories, Luisi writes (quoted work): «All share a major problem: each of these theories must start from a series of more or less arbitrary assumptions." In particular, the “compartmentalists” world has to assume that macromolecules (nucleic acids and enzymes) are already present in the prebiotic environment, the metabolic approach instead starts from the assumption that the enzymes already exist, and the RNA world is part of the assumption that a self-replicating RNA was available.
As we have repeatedly pointed out, making use of arbitrary assumption is unlikely to be a step forward and so, even in this case, there is no definition of the proto-organism.
So, in order to define a sustainable definition of proto-organism, instead of starting from arbitrary assumptions, we must start from certain data and possible scenarios in prebiotic era.
If the bacterial cell is the smallest vital entity, in order to identify the chemical bases of the proto-organism, can we start asking a question?
Which and how many macromolecules does a cell need to be considered living?
The bacterial cell is the smallest vital entity. Bacterial cells, however, do not all have the same number of macromolecules. The Escherichia coli DNA, for example, has about 3,000 genes and thus as many proteins as possible, while Pelagibacter Ubique contains about 1300. The smallest living bacterium known to date is a compulsive parasite, Mycoplasma Genitalium ccompartimentalists, supporters of the "RNA World" or metabolism, are convinced that a cell can live with a lower number of genes, and agree with a minimum genome of about 200 genes and as many proteins.
If this could have been the minimum cell content, if the proto-organism was something intermediate between the chemical period and the appearance of the cell, how could the proto-organism be differentiated from the minimum cell?
Let us then summarise the definition of life: metabolism, reproduction, evolution.
Which of these three properties belonged to the proto-organism?
Evolution is a characteristic of living organisms. So in order to have evolution we must have at least the minimum living organism, that is the cell. We don’t have the cell, but the proto-organism, and since it is not yet a living organism, evolution was absent. The proto-organism therefore had to be metabolism and reproduction. The point is that evolution comes from reproduction, if there is no evolution it’s because there is no reproduction and therefore the proto-organism could not contain the reproduction but only metabolism.
Can you separate metabolism and reproduction in a proto-organism?
According to Mario Ageno, "Biofisica 3" 1984, a system of only metabolism would have no biological significance because it would soon be dissipated in the environment without leaving any inheritance or trace. According to Ageno, the ability to reproduce is an indispensable feature for any system. On the other hand, as Dorothy Crawford explains about Viruses in the “Il nemico invisibile. Storia naturale dei virus”, there can be no reproduction without metabolism. Viruses are reproduced by exploiting host cell metabolism and if they do not find a host cell, they decompose.
So metabolism and reproduction cannot be separated, but proto-organism cannot contain reproduction. How do we get out of this dilemma?
The problem, as is often the case, is a terminology issue. The reproduction term contains the replication term, that is, a cell before reproduction must replicate its genome. Living organisms reproduce, molecules replicate. The Proto-organism is not a living organism and therefore does not reproduce. The term reproduction in general terms is often used, even for viruses. In fact, viruses within the cell do not reproduce but are replicated, ie they use the metabolic apparatus to replicate their own genome and increase the number until they stifle the cell. Hence, the proto-organism could not be a metabolic-reproductive system because reproduction is a feature of life, but it must have been a metabolic-replicative system. In other words, the proto-organism in order to survive only need, through a rudimentary metabolism, to replicate the damaged molecules.
So, if the proto-organism was a metabolic-replicative system, did it still needed a genome of 200 genes, needed for the minimum cell?
In summary, one is to look at which features of present living organisms may differ or be simpler in the proto-organism. Since there are different opinions on these topics, among several options, following Ockham's razor, we must choose the simplest and most credible one. We recall that William Ockham was a Franciscan Friar of the 14th century, and the Occam Razor principle is traced back to him: one must always start from simple, obvious assumptions and then add complexity if necessary. Certainly, it is not a universal principle but in our case it may be useful.
1) All researchers believe that the proto-organism originated in closed compartments.
As we have already explained, some scientists believe that these compartments were polymeric membranes. They, however, start from the assertion that the basic macromolecules (nucleic acids and proteins) already exist in the environment, and thus do not explain how these molecules formed. Furthermore, it is not known how these molecules have accumulated selectively within the membranes.
According to J. B. Bernal (post n.8), the compartments were, instead, cavities and intercrystalline spaces within clay granules. In these compartments constantly in contact with the outer environment, could accumulate and interact the molecules necessary for the origin of the proto-organism.

 In addition, macromolecules dispersion in the outer environment or their demolition due to ultraviolet rays could be avoided. It should be noted that the possibility of accumulation of simple molecules and polymer syntheses within the clay has been widely demonstrated in various researches. 
 This hypothesis on the compartments, shared by several researchers, seems more credible because it does not start from any assumption.
If the proto-organism originated within clay cavities, it was not necessary in that first phase to have the proto-cell membrane. If the latter element was absent, the genes and proteins necessary for its replication were absent, the genome had to be reduced by some units.
2) In all living organisms a nucleic acid, DNA, has the function of archiving genetic information. DNA portions, the genes, are transcribed in messenger nucleic acid, mRNA. It is the mRNA that translates protein information.
Has the DNA always existed? Almost all scientists today agree with what Mario Ageno wrote at the beginning of the 1980s in the chapter entitled “Dai precursori al proto-organismo” (quoted work). He made a depth analysis on the subject and wrote: «It is conceivable that at the beginning the transcription did not exist. A single nucleic acid with a single propeller could simultaneously carry out the chemical information archive function and actively intervene in synthesis operations». If the DNA was absent, the group of proteins necessary for its replication was absent. The genome of the proto-organism get much more simpler, at least by a dozen units.
3) Protein synthesis (post 27) is a fairly complex process. It needs a RNA messenger, transport RNA (adaptors), a ribosome and protein synthesis enzymes. Could such a system be present in the proto-organism?
Ageno still writes: «It is conceivable, indeed practically certain, that the ribosome, if it existed, was initially different from now, reducing itself only to the nucleic component. But it is also possible that at the beginning the ribosome did not exist and the synthesis occurred by interaction between the RNA and the loaded adapters with their amino acids. It is likely that the adapters, possibly simpler than the current ones, existed from the beginning. Otherwise, it would be necessary to postulate specific direct interactions between nucleotide and amino acid triplets, which do not seem to exist at least with sufficient intensity and specificity to influence decisively on the alignment of amino acids in the protein [...] ». Now, since here it is believed that in prebiotic period a direct and specific interaction between the tri-nucleotide and the amino acid existed (post 27), it meant even tRNA were absent.
The ribosome of the present bacteria contains about 50 proteins. The tRNA need at least 20 specific enzymes to bind each amino acid to each tRNA. Once aligned the tRNA, several other enzymes are needed to bind the amino acids in the polypeptide. If all this complex system did not exist, if the tRNA were absent, the proteins, and therefore the genes needed for their synthesis, were also absent, the genome of the proto-organism is therefore considerably reduced.
Ultimately, an approximate calculation of the above points leads to the conclusion that proto-organism could begin their existence with a genome of about 100 genes and as many proteins.
We then begin from the hypothesis that the port-organism contained a genome of RNA of about 100 genes.
As we have already mentioned (post 29), around 1970, the hypothesis that proteins were made up of domains, that is, a sequence of amino acids that is preserved during evolution, has been advanced. In 1974, Rossman identified a domain of about 70 amino acids present in many enzymes and suggested that even this domain was of prebiotic origin (Russell F. Doolittle, “Le Proteine”, Science 1985). But many scientists today believe that the domains in prebiotic era were smaller and consisted mainly of -Helix of about 20 amino acids (Mike Williamson, “Come funzionano le proteine” 2013).
Now, for every gene a protein, if the 100 genes encode for 100 proteins through 20 amino acids, what was the size of the genome of the proto-organism?
According to the genetic code, three triplets (ie three nucleotides) encode an amino acid (3: 1), so to specify 100 proteins of 20 amino acids, meaning 2000 amino acids, a 6,000-nucleotide genome is required. Let us consider for example the image of one of the four nucleotides: Adenosine-5-phosphate

So to give rise to a genome of 100 genes, 6000 of these nucleotides should have spontaneously and fairly bounded. No chemist and no biologist believes in the possibility of forming such a large molecule in prebiotic times. We can certainly conclude that such a genome did not exist at the beginning. It is very likely that when the proto-organism began to move its first steps, within it instead of one and only genome of 100 genes, there were 100 genes independent, separate from one another, each encoding a protein.
Therefore we can conclude as follows:
The proto-organism originated within clay cavities, where the essential substances for the origin of life accumulated and interacted. It was in constant contact with the environment for the supply of the substances necessary for its chemical evolution. There was still no DNA as a genetic information archive, nor did a single RNA genome carry out the dual function of archive of genetic information and protein synthesis and there were no tRNA for the transport of amino acids.
The proto-organism had to be composed of single RNA genes, about 100, initially completely independent, and about 100 proteins. Protein and RNA constituents, and small organic molecules from the outside environment, had to be present inside the proto-organism. RNA synthesis and protein synthesis took place by direct interaction between amino acids of a protein and nucleotides, and between RNA nucleotides and amino acid respectively (post 29).
Once defined the proto-organism, two questions arise:
How did the proto-organism originate from inanimate matter?
How did the passage from the proto-organism to the cell occur?

Giovanni Occhipinti

Translated by: Sydney Isae Lukee

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