The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry

Abstract

It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a ‘view from here’ that we term the Circlet hypothesis as part of a broader Ring World. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We can conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution to the fundamental problems that probably confront both the earliest cells and the most recent ones.

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

“…Once a regulatory system with many interactions between essential components has been constructed, it is well-nigh impossible to replace it completely. With this, and with the above criteria in mind, we have tried to formulate hypotheses for the regulation of the cell cycle that can be grounded in a plausible origins-of-life scenario [ 53 , 178 , 179 ]. Since this system evolved before the emergence of sophisticated macromolecules, it probably depended on the physical chemistry of the interactions of a host of simple molecules in the form of “composomes” [ 180 ], the putative ancestors of hyperstructures.…”

“…And a related question is whether the metabolites themselves are directly part of initiation and/or replication hyperstructures, not just by binding to the constituent proteins (as in the case of DnaA and cAMP [ 49 ]) or by being used to modify the protein (as in the case of DnaA and acetyl-CoA), but also by binding directly to RNA or DNA. If metabolites were indeed to bind the origin region, this would make the connection with the Ring World , an origins-of-life scenario in which small, double-stranded DNA rings were selected firstly because they catalysed the reactions of central carbon metabolism [ 53 ].…”

“…It could also be argued that it would have made sense for the earliest protocells to have had the same signalling mechanism leading to both DNA replication and cell division. This is because the RNA and/or DNA in these protocells was probably short and, in the Ring World scenario, in the form of a population of ds RNA/DNA rings, each of which catalysed a different reaction [ 53 , 96 ]; hence, the fundamental problem that protocells had to solve was not how to divide after replicating a long stretch of DNA, but rather how to proceed successfully through a complete cell cycle, which is a single decision. Norris has proposed that making this decision requires both intensity-sensing (does a cellular constituent risk becoming limiting for growth?)…”

Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock

“…This scenario would t well with the phase transitions illustrated in Figure 3, which could lead not to similar daughters but rather to one daughter with condensed, inactive, degradation-resistant hyperstructures and the other with extended, active, fragile hyperstructures. 9. makes a connection with origins of life hypotheses in which cycles of wetting and drying can generate ring-like structures of RNA (Hassenkam et al, 2020) and possibly rings of double-stranded DNA with properties that would include glycolysis and catalysing DNA replication (Norris & Demongeot, 2022). In this 'Ring World' hypothesis, an early cell would have contained many rings with complementary functions and the successful growth of this cell would, in the water-clock hypothesis, have led to a decrease in water availability and the simultaneous replication of all the cell's rings.…”

Primitive Oligomeric RNAs at the Origins of Life on Earth

“…More recently, it was suggested to integrate the two theories with each other. DNA, enzymes and lipids were assumed to have interfered early with the engineering of the primitive RNAs [26] in order to give it a selective advantage over purely chemical systems [27][28][29][30][31][32][33][34][35][36]. This interpretation combines (i) the existence of a form of storage within primitive RNAs, also making it possible to promote peptide synthesis and the appearance of proto-genes consisting of combinations of fragments of primitive RNAs, (ii) the random inclusion of new RNA materials giving birth progressively to proteins ensuring biosynthesis and replication of DNA, (iii) the formation of lipid membranes compartmentalizing the spatial location of the functions (i) and (ii).…”