Wednesday, September 20, 2017

From RNA world to RNA-tRNA world to DNA-RNA-protein world: how it went?

I encountered a highly interesting work related to the emergence of RNA world: warmly recommended. For a popular article see this.

First some basic terms for the possible reader of the article. There are three key enzymes involved in the process which is believed to lead to a formation of longer RNA sequences able to replicate.

  1. Ribozyme is a piece of RNA acting as catalyst. In RNA world RNA had to serve also as a catalyst. In DNA world proteins took this task but their production requires DNA and transcription-translation machinery.

  2. RNA ligase promotes a fusion of RNA fragments to a longer one in presence of ATP transforming to AMP and diphospate and giving metabolic energy presumably going to the fusion. In TGD fUniverse this would involve
    generation of an atom (presumably hydrogen) with non-standard value of heff=n×h having smaller binding energy scales so that ATP is needed. These dark bonds would be involved with all bio-catalytic processes.

  3. RNA polymerase promotes a polymerization of RNA from building bricks. It looks to me like a special kind of ligase adding only single nucleotide to an existing sequence. In TGD Universe heff=n×h atoms would be involved as also magnetic flux tubes carrying dark analog of DNA with codons replaced with dark proton triplets.

  4. RNA recombinase promotes RNA strands to exchange pieces of same length. Topologically this corresponds to two reconnections occurring at points defining the ends of piece. In TGD Universe these reconnections would occur for magnetic flux tubes containing dark variant of DNA and induce the chemical processes at the level of chemistry.

Self ligation should take place. RNA strands would serve as ligases for the generation of longer RNA strands. The smallest RNA sequences exhibiting self-ligation activity was found to be 40-nucleotide RNA and shorter than expected. It had lowest efficiency but highest functional flexibility to ligate substrates to itself. R18 - established RNA polymerase model - had highest efficiency and highest selectivity.

What I can say about the results is that they give support for the notion of RNA world.

The work is related to the vision about RNA world proposed to precede DNA-RNA-protein world. Why I found it so interesting is that it relates to on particular TGD inspired glimpse to what happened in primordial biology.

In TGD Universe it is natural to imagine 3 worlds. RNA world, RNA-tRNA world, and DNA-RNA-protein world. For an early rather detailed version of the idea about transition from RNA world to DNA-RNA-proteins world but not realizing the tRNA-RNA world as intermediate step see this.

  1. RNA world would contain only RNA. Protein enzymes would not be present in RNA world and RNA itself should catalyze the processes needed to for polymerization, replication, and recombination of RNA. Ribozymes are the RNA counterparts of enzymes. In the beginning RNA would itself act as ribozymes catalyzing these processes.

  2. One can also try to imagine RNA-tRNA world. The predecessors of tRNA molecules containing just single amino-acid could have catalyzed the fusion of RNA nucleotide to a growing RNA sequence in accordance with the genetic code. Amino-acid sequences would not have been present at this stage since there would be no machinery for their polymerisation.

  3. My own proposal was that transition from RNA world to DNA-RNA-protein world took place as a revolution. Amino-acids of tRNA catalyzing RNA replication stole the place of RNA sequences as end products from RNA replication. The ribosome started to function as a translator of RNA sequences to amino-acid sequences rather than replication of them to RNAs! The roles of protein and RNA changed! Instead of RNA in tRNA the amino-acid in tRNA joined to the sequence! The existing machinery started to produce amino-acid sequences! Servant became the master!

    Presumably the modification of ribosome involved addition of protein parts to ribosome, which led to a quantum critical situation in which the roles of proteins and RNA polymers could change temporarily. When protein production became possible even temporarily, the produced proteins began to modify ribosome further to become even more favorable for the production of proteins.

    But how to produce the RNA sequences? The RNA replication machinery was stolen in the revolution. DNA had to do that via transcription to mRNA! DNA had to emerge before the revolution or at the same time and make possible the production of RNA via transcription of DNA to mRNA. DNA could have emerged during RNA-tRNA era together with reverse transcription of RNA to DNA with RNA sequences defining ribozymes acting as reverse transcriptase. This would have become possible after the emergence of predecessor of cell membrane. After that step DNA sequences and amino-acid sequences would have been able to make the revolution together so that RNA as the master of the world was forced to become a mere servant!

    The really science fictive option would be identification of the reverse transcription as time reversal of transcription. In zero energy ontology (ZEO) this option can be considered at least at the level of dark DNA and RNA providing the template of dynamics for ordinary matter.

How this could be tested? Could for instance ribosome be modified to a state in which RNA is translates to RNA sequences rather than proteins?

See the chapter Evolution in Many-Sheeted Space-Time of "Genes and Memes".

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

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