Revenant: a database of resurrected proteins

Abstract

Revenant is a database of resurrected proteins coming from extinct organisms. Currently, it contains a manually curated collection of 84 resurrected proteins derived from bibliographic data. Each protein is extensively annotated, including structural, biochemical and biophysical information. Revenant contains a browse capability designed as a timeline from where the different proteins can be accessed. The oldest Revenant entries are between 4200 and 3500 million years ago, while the younger entries are between 8.8 and 6.3 million years ago. These proteins have been resurrected using computational tools called ancestral sequence reconstruction techniques combined with wet-laboratory synthesis and expression. Resurrected proteins are commonly used, with a noticeable increase during the past years, to explore and test different evolutionary hypotheses such as protein stability, to explore the origin of new functions, to get biochemical insights into past metabolisms and to explore specificity and promiscuous behaviour of ancient proteins.

Figure 1

Schematic representation of the different steps to obtain resurrected proteins. The first step involves sequence similarity searches of a given protein to obtain a set of homologous sequences, involving the ancestral nodes to be studied. For example, one could be interested in studying biochemical properties of the studied protein in the last common ancestor for all vertebrates. Using these sequences, it is possible to estimate a phylogenetic tree to define the ancestral node to be reconstructed. In the second step, ancestral sequence reconstruction techniques are applied to estimate most probable sequences in the studied node. The third step involves the ancestral sequence synthesis. This sequence is then inserted into a vector, cloned, expressed and purified (fourth step). The fifth and final step involves a series of biochemical and biophysical characterization.

Figure 2

Two different browsing capabilities are available in Revenant. In the first one (top panel) proteins are listed sequentially using their RV codes. In the second browser (bottom panel) we display the Revenant proteins in an Earth’s timeline showing important biological events since the origin of life.

Figure 3

Screenshot of Revenant web server showing the home page and search utilities.

Figure 4

Main entry page. Each entry starts with a title followed by a brief explanation of the biological relevance of the resurrected protein. Additionally, each entry has fields regarding ancestral sequence reconstruction, information about their structures, biochemical and biophysical parameters and, finally, the primary citation.