Evolution and RNA Relics. A Systems Biology View

Abstract

The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.

Emergence of a “Cyclosome” in a Primitive Network Capable of Building “Infinite” Proteins

“…The 25 selected rings satisfy two opposite constraints corresponding to a min-max problem: (i) to be as short as possible, and (ii) to contain one and only one triplet corresponding to each amino acid synonymy class. The latter constraint would allow the rings to serve as a “matrimonial agency” concentrating amino acids in the vicinity of the ring and thereby favoring the links between any pair of them via peptide bonds [48,49,50,51,52,53,54,55]. The 25 RNA rings selected can be considered as ancestors of the tRNA of the 22 AAs including Pyrrolysine and Selenocysteine (Figure 3), with Serine counted twice, and Tyrosine and Aspartic Acid able to replace C by U in their tRNA anticodons [56,57].…”

General architecture of a genetic regulatory network. Applications to embryologic control

“…For satisfying the constraints above, the RNA AB must be circular and contain at least 20 triplets. The minimal solution is given in (Demongeot and Besson, 1983;Demongeot et al 2006Demongeot et al , 2008aDemongeot et al , 2009aDemongeot et al , 2009c. The corresponding RNA AB sequence can be given in circular or hair-pin form and could be considered as the ancestor of the present tRNA loops.…”

RNA Relics and Origin of Life

“…When the structure of the molecule of heredity was revealed by X-ray crystallography by R. Franklin and M. Wilkins [ 51 , 52 ] and then characterized as a double helix structure by J. Watson and F. Crick [ 53 ] in 1953, the scientific community had the possibility to search and find a molecular basis for explaining first the correspondence between DNA and proteins and then the now well-known processes of transcription and translation that allow protein production by the cell machinery [ 54 – 56 ]. G. Gamow, based on this new knowledge, proposed in 1954 his “diamond code” [ 57 ].…”

“…The researches concerning the origins of life and the manner the first polynucleic assemblies, the XNAs (PNAs for peptide nucleic acids, RNAs or DNAs), coding for the first peptides or proteins followed a similar reasoning, i.e., were also based on the principle of adapter molecules. These tRNAs ancestors would have been similar to the “aptamers” obtained in the in vitro evolution of amino-acids ligands [ 56 , 60 – 64 ]. Some chemists however have continued to work on a direct stereochemical interaction between amino-acids and DNA, for some of them because tRNAs were not yet or just discovered and later, for the others, because they thought aptamers or other adapters are too complicated for explaining DNA translation at the early stages of “life” and especially before, during the prebiotic ages [ 54 , 65 – 68 ].…”