Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis

Abstract

Evolution of proteins encoded in nucleotide sequences began with the advent of the triplet code. The chronological order of the appearance of amino acids on the evolution scene and the steps in the evolution of the triplet code have been recently reconstructed (Trifonov, 2000b) on the basis of 40 different ranking criteria and hypotheses. According to the consensus chronology, the pair of complementary GGC and GCC codons for the amino acids alanine and glycine appeared first. Other codons appeared as complementary pairs as well, which divided their respective amino acids into two alphabets, encoded by triplets with either central purines or central pyrimidines: G, D, S, E, N, R, K, Q, C, H, Y, and W (Glycine alphabet G) and A, V, P, S, L, T, I, F, and M (Alanine alphabet A). It is speculated that the earliest polypeptide chains were very short, presumably of uniform length, belonging to two alphabet types encoded in the two complementary strands of the earliest mRNA duplexes. After the fusion of the minigenes, a mosaic of the alphabets would form. Traces of the predicted mosaic structure have been, indeed, detected in the protein sequences of complete prokaryotic genomes in the form of weak oscillations with the period 12 residues in the form of alteration of two types of 6 residue long units. The next stage of protein evolution corresponded to the closure of the chains in the loops of the size 25-30 residues (Berezovsky et al., 2000). Autocorrelation analysis of proteins of 23 complete archaebacterial and eubacterial genomes revealed that the preferred distances between valine, alanine, glycine, leucine, and isoleucine along the sequences are in the same range of 25-30 residues, indicating that the loops are primarily closed by hydrophobic interactions between the ends of the loops. The loop closure stage is followed by the formation of typical folds of 100-200 amino acids, via end-to-end fusion of the genes encoding the loop-size chains. This size was apparently dictated by the optimal ring closure for DNA. In both cases the closure into the ring (loop) rendered evolutionarily advantageous stability to the respective structures. Further gene fusions lead to the formation of modern multidomain proteins. Recombinational gene splicing is likely to have appeared after the DNA circularization stage.

One scorpion, two venoms: Prevenom ofParabuthus transvaalicusacts as an alternative type of venom with distinct mechanism of action

“…We observed that small peptides of 900-1,200 Da in size are more prevalent than other components; the second most abundant group of peptides is the K ϩ channel blockers (3-to 4-kDa peptides), followed by the 6-to 7-kDa peptides classically targeting the Na ϩ channels that are the least abundant group in the prevenom. It is noteworthy to mention that this pattern is in agreement with the general evolutionary formula of ''from simple to more complex'' (28).…”

Conserved Ser residues, the Shutter Region, and Speciation in Serpin Evolution

“…The primordiality of TCN codons compared with AGY codons at conserved positions (11,12) and the species segregation of the lineages indicate that the TCN lineage was older and gave rise to the AGY lineage. We used the method previously described for serine protease lineages (6) to identify the "parent inhibitor" (the modern inhibitor most similar to the putative ancestral inhibitor) for the AGY lineage.…”

Formamide and the origin of life

“…The nature of the very first peptides has been indicated and the reasons for the assignment have been presented [154,155]. These very first peptides supposedly were (Ala) 7 and (Gly) 7 , encoded by (GCC) 7 and (GGC) 7 , the two strands of the earliest RNA duplex genes [154,155].…”

“…These very first peptides supposedly were (Ala) 7 and (Gly) 7 , encoded by (GCC) 7 and (GGC) 7 , the two strands of the earliest RNA duplex genes [154,155]. Hence the relevance of GCCn*GGCn replication studies.…”