Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code

Abstract

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.

Evolution of initiator tRNAs and selection of methionine as the initiating amino acid

“…In contrast to the other amino acids, the abundance of Met has not changed from LUCA to modern genomes. 56 For evolution of a specialized elongator tRNA Met from tRNA i , it would require several drastic changes in the specific features of tRNA i making the whole phenomenon an unlikely event. Therefore, the specialized elongator tRNA Met might have evolved from other tRNAs.…”

Protein Flexibility and Coiled-Coil Propensity: New Insights Into Type III and Other Bacterial Secretion Systems

“…Other secreted proteins have an average value of 0.50. The ratio for cytoplasmic T3SS proteins is 0.55; the average ratio in proteomes is 0.58 based on the amino acid frequencies of order-and disorder-promoting residues (Brooks et al, 2002); significantly lower values, as in the case of the N-termini of T3SS effectors, indicate a propensity for disorder. The only structured N-terminal region of a T3SS effector is that of YopH.…”

Cyclosporin A Impairs the Secretion and Activity of ADAMTS13 (A Disintegrin and Metalloprotease with Thrombospondin Type 1 Repeat)

“…Mammalian cells contain three classes of PPIs: parvulins, cyclophilins (Cyps), and FK506-binding proteins (8). ADAMTS13, harboring 118 prolines, contains a higher number of proline residues in comparison with human proteins (9). It is therefore plausible that PPIases may play an important role in the folding and maturation of this protein.…”

“…S2, A and B). The total number of proline residues in ADAMTS13 is 118, thus constituting 8.3% of all the amino acids in this protein, whereas the average proline usage in vertebrate proteins is about 5% and in human proteins ϳ6.17% (9).…”