Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code

Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an ~16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to ~16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation.

Temperature and polarity based evolutionary model of the ribosomal complex in Thermus thermophilus and Escherichia coli

The ribosome is considered a molecular fossil of the RNA world and is the oldest molecular machinery of living cells responsible for translating genetic information encoded by messenger RNA(mRNA) to proteins. Currently not much is known regarding how these proteins were assembled and the potential biogeochemical environment that could have shaped their evolution. In order to answer these questions, a comprehensive analysis of the amino acid frequencies of 30S and 50S ribosomal sub-units occurring in thermophile Thermus thermophilus and mesophile Escherichia coli was performed. The amino acid frequencies in proteins are believed to have been shaped by their pre-biotic abundances in the universe and by heavy bombardment of meteorites on planet earth (4.5-3.8 Ga). Absence of amino acid residues such as cysteine and tryptophan in T.thermophilus and E.coli proteins hints towards the evolution of small and large subunits prior to the origin of metabolic pathways of amino acid synthesis possibly under anoxic and sulphur free conditions. Moreover, an underrepresentation of readily oxidizable amino acids such as methionine, tyrosine and histidine, indicates that these proteins could have evolved in a more reducing environment as was prevalent on early earth. A comparison of amino acid biases with universal UNIPROT estimates, indicates arginine and lysine overrepresentation, linking a role of these amino acids in ribosomal RNA binding and stabilization corresponding to the RNA world hypothesis whereby RNA molecules drove the assembly of living systems. The continuing prevalence of these amino acid biases in modern proteins reflects the functional stability of ancient proteins constructed during billions of years of evolution and provides glimpses into the evolution of the ancient amino acid code. Step-wise accretion models involving increasing complexity of the amino acid code and the ribosomal sub-units are proposed for T.thermophilus and E.coli, providing potential insights regarding the origin of ribosomes in a temperature dependent and polar environment.