Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.29.227728v1?rss=1

Authors: Davis, B. K.

Abstract:

Sequence homology in pre-divergence tRNA species revealed cofactor/adaptors cognate for 16 amino acids derived from oxaloacetate, pyruvate, phosphoglycerate, or phosphoenolpyruvate were related. Synthesis path-distances of these amino acids correlated with phylogenetic depth, reflecting relative residue frequency in pre-divergence sequences. Both metrics were thus aligned in the four sub-families of the Aspartate family, and misaligned in the small Glutamate family; a functional difference was noted and seen to parallel synthetase duality. Amino acid synthetic order, based on path-distances, indicate NH4+ fixer amino acids, Asp1, Asn2, and homologues, Glu1, Gln2, formed the first code. Together with a termination signal, they acquired all four triplet 4-sets in the XAN column (X, 5-prime coding site; N, any 3-prime-base). An invariant mid-A conformed with pre-code translation on a poly(A) template by a ratchet-equipped ribosome resulting in random, polyanionic polypeptides. Code expansion occurred in a compact (mutation minimizing) column-wise pattern, (XAN)to XCN to XGN to XUN; with increasing mean path-distance, (1.5) to 4 to 5 to 7 steps; amino acid side-chain hydro-phobicity, (+6.6)to -0.8 to -1.5 to-3.2 kcal/mol; codon:anticodon H bond enthalpy (selection for bond-strength), (-12.5)to -17.5 to -15.5 to -14.5 kcal/mol; and precursor-specific 5-prime-base, A, oxaloacetate, G, pyruvate/ oxalo-acetate, U, phosphoglycerate/oxaloacetate, C, oxoglutarate, forming horizontal code domains. Codon bias evidence corroborated the XCN to XGN step in expansion, and revealed row GNN coevolved with ANN, on correction for overprinting. Extended surface-attachment (Fajan-Paneth principle) by pro-Fd[5] and bilayer partitioning by H+ ATPase proteolipid-h1 subunit implicated expansion phase proteins in driving increases in side-chain hydrophobicity during code expansion. 3-prime-Base recruitment in pre-assigned codon boxes added six long (9- to 14-step) path amino acid, bearing a basic, or cyclic, side-chain; 3 of 4 polar, post-expansion amino acids acquired polar cluster NAN codons and 2 of 3 non-polar (Ile7 included) acquired non-polar cluster NUN codons, yieldng a split-box pair homology of p = 5.4x10-3. All eight overprinted codon boxes (GAYR for Asp1, Glu1 included) exhibit weak codon: anti-codon H-bond enthalpy, -14 kcal/mol or higher, in three of six distinct code enthalpy states.

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