A self-referential model for the formation of the genetic code

Abstract

A model for the formation of the genetic code is presented where protein synthesis is directed initially by tRNA dimers. Proteins that are resistant to degradation and efficient RNA-binders protect the RNAs. Replication becomes elongational producing poly-tRNAs from which the mRNAs and ribosomes are derived. Attributions are successively fixed to tRNAs paired through the perfect palindromic anticodons, with the same bases at the extremities (5'ANA: UNU 3'; GNG: CNC; principal dinucleotides, pDiN). The 5' degeneracy is then developed. The first pairs to be encoded correspond to the hydropathy correlation outliers (Gly-CC: Pro-GG and Ser-GA: Ser-CU) and to the sector of homogeneous pDiN, composed by two pyrimidines or two purines. These amino acids are preferred in the N-ends of proteins, stabilizers of proteins against catabolism and strong RNA-binders. The next pairs complete the sector of homogeneous pDiN (Asp, Glu-UC: Leu-AG and Asn, Lys-UU: Phe-AA). This set of nine amino acids forms the protein cores with the predominant aperiodic conformation. Next enter the pairs with mixed pDiN (one purine and one pyrimidine), the RY attributions composing the protein N-ends and the YR attributions the C-ends. The last pair contains the main punctuation signs (Ile, Met, iMet-AU: Tyr, Stop-UA). The model indicates that genetic information emerged during the process of formation of the coding/decoding system and that genes were defined by the proteins. Stable proteins constructed the nucleoprotein system by binding to the RNAs that produced them. In this circular rationale, genes are memories in a metabolic system for production of proteins that stabilize it. The simplicity and the highly deterministic character of the process suggest that the Last Universal Common Ancestor populations could be composed, in early stages, of lineages bearing similar genetic codes.

Genetic Hotels for the Standard Genetic Code: Evolutionary Analysis Based upon Novel Three-Dimensional Algebraic Models

“…These authors concluded that "the evolution of the genetic code, translation, and cellular organization itself follows a dynamic whose mode is, if anything, Lamarckian" (Vetsigian et al 2006). Another interesting non-Darwinian model for the evolution of the genetic code is the SelfReferential (SR) model (Guimarãez et al 2008a(Guimarãez et al , 2008b. This model regards the code as a consequence of the existence of proto-tRNAs, small prebiotic tRNA-like molecules: tRNA-like in the sense of having the ability to form dimers by base-pairing (through their proto-anticodons) and to receive the addition of other molecules to one end.…”

“…"Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today" (Woese 1968). In the SR model (Guimarãez et al 2008a(Guimarãez et al , 2008b, protein functions should also feedback positively upon the nucleic acids, thereby providing for a double link between genes and proteins, and both links being of equal weight. Therefore, in the SR model it does not make sense the idea of "selfish genes" or "selfish proteins."…”

“…However, in the model of Delarue (2008), the triplets NAN remained undefined until the SGC was frozen. On other comparisons, the complementary set of our Extended RNA code I, is the last set of codons to enter whereas in the SR model (Guimarãez et al 2008a(Guimarãez et al , 2008b this set is considered to be as the primordial set.…”

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

“…The self-referential (SR) process, of protein products looping back to stabilize and stimulate the nucleic acids -producers, thereafter memories in RNPs -has already received contributions from diverse sources, beyond the proposition of the model (SRM) [108,109]. Ribosomal proteins belong to the category of Intrinsically Disordered [42], which is a character of the early encodings in the SRM.…”

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

“…The self-referential (SR) process, of protein products looping back to stabilize and stimulate the nucleic acids -producers, thereafter memories in RNPs -has already received contributions from diverse sources, beyond the proposition of the model (SRM) [93,94]. Ribosomal proteins belong to the category of Intrinsically Disordered [35], which is a character of the early encodings in the SRM.…”