Evolution of protein families: Is it possible to distinguish between domains of life?

Abstract

Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability in molecular substitution rates, however, we still do not know whether such variability is due to species-specific trends at a genomic scale, or whether it can be attributed to the fluctuations inherent in any stochastic process. Here, we study the statistical properties of gene and protein family sizes in order to quantify the long time scale evolutionary differences and similarities across species. We first determine the protein families of 209 species of bacteria and 20 species of archaea. We find that we are unable to reject the null hypothesis that the protein family sizes of these species are drawn from the same distribution. In addition, we find that for species classified in the same phylogenetic branch or in the same lifestyle group, family size distributions are not significantly more similar than for species in different branches. These two findings can be accounted for in terms of a dynamical birth, death, and innovation model that assumes identical protein family evolutionary rates for all species. Our theoretical and empirical results thus strongly suggest that the variability empirically observed in protein family size distributions is compatible with the expected stochastic fluctuations for an evolutionary process with identical genomic evolutionary rates. Our findings hold special importance for the plausibility of some theories of the origin of eukaryotes which require drastic changes in evolutionary rates for some period during the last two billion years.

Origin of eukaryotes as a symbiosis of parasitic α-proteobacteria in the periplasm of two-membrane-bounded sexual prekaryotes

“…All prokaryote-to-eukaryote transition models: (1) assume that prokaryotes (i.e., bacteria, archaea and/or prokaryotic chimeras, hybrids and/or associations) were direct ancestors of eukaryotes for what no direct evidence exists; 16 (2) do not explain precisely how exactly eukaryotic specific proteins 60 and features with no prokaryotic counterparts arose; 31 (3) have to suggest that either LECA or LACA underwent through selectively costly stage with membrane(s) composed of a mixture of archaeal and bacterial lipids, which is (are) less stable than membranes composed of only archaeal or bacterial lipids; 2,3 (4) have to propose dramatic and unrealistic change in rates of protein evolution in only one (two or three) prokaryotic species, 31 while no such drastic change in rates of evolution has been detected by recent analysis of protein families; 61 (5) ignore to explain the origin of meiosis and sex. 62 An additional pitfall of models proposing that an archaeal cell was involved in the origin of eukaryotes (all models mentioned above except for G + -bacterial origin of Eukarya and Archaea) is that they do not explain why phylogenies of informational genes place Eukarya as a sister group to Archaea, and not within the diversity of modern archaea.…”

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two‐domain constructs: A computational characterization of novel chimeric proteins

“…This means that subunits, or domains, can be identified and assigned to specific functional or structural properties. Modular organization of domains to generate proteins with specific functions is a plausible evolution concept (also explored and proven by bioinformatics methods). Modular composition of proteins offers a large number of functional possibilities at relatively low energy cost, compared to the evolution of a new protein to serve a specific function.…”