Preprint Hypothesis Version 4 This version is not peer-reviewed

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

Version 1 : Received: 28 March 2020 / Approved: 29 March 2020 / Online: 29 March 2020 (04:08:22 CEST)
Version 2 : Received: 1 April 2020 / Approved: 2 April 2020 / Online: 2 April 2020 (05:16:09 CEST)
Version 3 : Received: 17 April 2020 / Approved: 19 April 2020 / Online: 19 April 2020 (04:00:24 CEST)
Version 4 : Received: 11 July 2020 / Approved: 12 July 2020 / Online: 12 July 2020 (14:28:35 CEST)
Version 5 : Received: 26 July 2020 / Approved: 26 July 2020 / Online: 26 July 2020 (17:40:23 CEST)
Version 6 : Received: 6 August 2020 / Approved: 7 August 2020 / Online: 7 August 2020 (06:53:34 CEST)

How to cite: Xie, P. The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code. Preprints 2020, 2020030419 (doi: 10.20944/preprints202003.0419.v4). Xie, P. The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code. Preprints 2020, 2020030419 (doi: 10.20944/preprints202003.0419.v4).

Abstract

More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries in life science, although a plenty of theories have been proposed so far, as none can explain satisfactorily why the genetic code evolved in such a way, especially in the context of the biochemical system, a relation of part to whole. Here, a new hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system of the protocell. This hypothesis shows how primitive life with its genetic code emerged through a series of processes from energy flow to information communication mediated by ATP. First, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the extant biochemical systems. Second, ATP serves as not only an energy carrier but also an informatization molecule, as ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating biochemical innovation in the protocell from energy transformation to informatization, a process for creating and managing information. Informatization was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

Subject Areas

the origin of the genetic code; the ATP hypothesis; the first key building block in the probiotic soup; coevolution of the genetic code with biochemical system; from energy transformation to informatization and structuralization; cyclizing of polynucleotides and polypeptides

Comments (1)

Comment 1
Received: 12 July 2020
Commenter: Ping Xie
Commenter's Conflict of Interests: Author
Comment: 1. This vesion answered three questions from experts:
"First, in your hypothesis, ATP is synthesized by the primitive photosynthesis chemical system, and is the initiator of other nucleotides, and also promotes the formation of peptide and RNA polymers.  However, research from Sutherland's group gives a plausible pre-biotic origin of pyrimidine nucleotides that does not depend on ATP (or purines). And these earliest components of nucleotides (even their polymers) can be synthesized chemically, which seems a lot earlier than the appearance of the primitive photosynthesis system. Secondly, are there any experimental evidences supporting that other nucleotides were derived from ATP?Thirdly, does this primitive photosynthesis system operate to produce ATP without the involvement of proteins at all?  How was the photosynthesis system propagated in early life without involving DNA, or even RNA?".
I added two paragraphs:
"It may be argued that prebiotic origin of pyrimidine nucleotides does not depend on ATP, and that these earliest components of nucleotides (even their polymers) can be synthesized chemically, which seems a lot earlier than the appearance of the primitive photosynthesis system [27, 28]. However, the fact that nucleotides were present in the prebiotic soup without the aid of photosynthesis does not deny the possibility that production of ATP coevolved with photosynthesis in the protocell, leading to the completion of the biochemical system as well as its genetic codes in current cells. A, G, C, and T/U or other nucleotides might have occurred in the prebiotic soup, but only ATP was successfully selected as the energetic product of photosynthesis in the protocell. This may either be random or inevitable due to e.g. molecular compatibility. Eventually, with the development of biochemical system, ATP began to drive energetically the formations of other nucleotides using simple molecules such as amino acids, glutamine, one carbon unit, CO2 etc.  
It may also be argued whether this primitive photosynthesis system operate to produce ATP without the involvement of proteins at all and how the photosynthesis system was propagated in early life without involving DNA, or even RNA. Actually, various life’ building brocks (e.g. amino acid, purines, pyrimidines) are found to be present in meteorolites [29], indicating that nucleotides could be present or easily formed in the prebiotic soup. The protocell innovated the photosynthesis system to produce ATP, which later has been processed efficiently and regularly with the aids of proteins and RNA/DNA."
2. I added a table as suggested by an expert;
3. I deleted figures 2 and 3, as suggested by an expert.

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