Genetic Code Evolution Reconstructed with Aligned Metrics

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’ coding site; N, any 3’-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) columnwise pattern, (XAN) ➔ XCN ➔ XGN ➔ XUN; with increasing mean path-distance, (1.5) ➔ 4 ➔ 5 ➔ 7 steps; amino acid side-chain hydrophobicity, (+6.6) ➔ −0.8 ➔ −1.5 ➔ −3.2 kcal/ mol; codon:anticodon H bond enthalpy (selection for bond-strength), (−12.5) ➔ −17.5 ➔ −15.5 ➔ −14.5 kcal/ mol; and precursorspecific 5’-base, A, oxaloacetate, G, pyruvate/oxaloacetate, U, phosphoglycerate/oxaloacetate, C, oxoglutarate, forming horizontal code domains. Codon bias evidence corroborated the XCN ➔ XGN step in expansion, and revealed row GNN coevolved with ANN, on correction for overprinting. Extended surfaceattachment (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’-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 = 5.4×10-3. All eight overprinted codon boxes (GAYR for Asp1, Glu1 included) exhibit weak codon:anticodon H-bond enthalpy, −14 kcal/mol or higher, in three of six distinct code enthalpy states.

ProfileGrids solve the large alignment visualization problem: influenza hemagglutinin example

Large multiple sequence alignments are a challenge for current visualization programs. ProfileGrids are a solution that reduces alignments to a matrix, color-shaded according to the residue frequency at each column position. ProfileGrids are not limited by the number of sequences and so solves this visualization problem. We demonstrate the new metadata searching and grep filtering features of the JProfileGrid version 2.0 software on an alignment of 11,900 hemagglutinin protein sequences. JProfileGrid is free and available from http://www.ProfileGrid.org.