The thermostability and specificity of ancient proteins

Abstract

Were ancient proteins systematically different than modern proteins? The answer to this question is profoundly important, shaping how we understand the origins of protein biochemical, biophysical, and functional properties. Ancestral sequence reconstruction (ASR), a phylogenetic approach to infer the sequences of ancestral proteins, may reveal such trends. We discuss two proposed trends: a transition from higher to lower thermostability and a tendency for proteins to acquire higher specificity over time. We review the evidence for elevated ancestral thermostability and discuss its possible origins in a changing environmental temperature and/or reconstruction bias. We also conclude that there is, as yet, insufficient data to support a trend from promiscuity to specificity. Finally, we propose future work to understand these proposed evolutionary trends.

Evolutionary trend toward kinetic stability in the folding trajectory of RNases H

“…In addition, such comparative studies are often limited by epistatic effects, which complicate the identification of sequence determinants and mechanisms (12, 13). More importantly, these extant homologs can reveal only the outcomes of an evolutionary process, and not the mechanism by which different properties arose from a common ancestral state (14).In contrast, ancestral sequence reconstruction (ASR) allows direct interrogation of a protein's history by using evolutionary relationships and sequences of modern homologs to statistically infer ancestral states within a family's phylogenetic tree (12)(13)(14). Characterizing these ancestral proteins will reveal trends in folding properties and also help identify the evolutionary demands on folding.…”

“…This information then can be used to engineer proteins with desired folding properties. ASR has already provided important insights into evolutionary trends in stability, specificity, and other biophysical properties (12)(13)(14)(15)(16)(17)(18)(19)(20).Previously, we used ASR to study the thermostability of the ribonuclease H (RNase H) family and demonstrated divergent trends in thermostability along mesophilic and thermophilic lineages (16). Here we examined the folding mechanism and associated rates of these reconstructed ancestral RNases H. The folding pathway of the two extant homologs, Escherichia coli RNase H (ecRNH) and Thermus thermophilus RNase H Significance Because protein folding is crucial to proper cellular function, there must be evolutionary pressures on how a protein achieves and maintains its folded structure.…”

“…In addition, such comparative studies are often limited by epistatic effects, which complicate the identification of sequence determinants and mechanisms (12,13). More importantly, these extant homologs can reveal only the outcomes of an evolutionary process, and not the mechanism by which different properties arose from a common ancestral state (14).…”

“…In contrast, ancestral sequence reconstruction (ASR) allows direct interrogation of a protein's history by using evolutionary relationships and sequences of modern homologs to statistically infer ancestral states within a family's phylogenetic tree (12)(13)(14). Characterizing these ancestral proteins will reveal trends in folding properties and also help identify the evolutionary demands on folding.…”

“…This information then can be used to engineer proteins with desired folding properties. ASR has already provided important insights into evolutionary trends in stability, specificity, and other biophysical properties (12)(13)(14)(15)(16)(17)(18)(19)(20).…”