Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

Abstract

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Keywords: Rubisco; ancestral sequence reconstruction; carbonic anhydrase; origins; palaeophenotype.

Figure 1.

Criteria for palaeophenotype reconstruction in the laboratory by generating hybrid ancient–modern bacterial systems.

Figure 2.

Maximum-likelihood phylogenetic reconstruction of carbonic anhydrase (CA). The 492 CA homologues retrieved from 388 representative genomes were aligned with mafft-linsi and a maximum-likelihood phylogeny was inferred from the alignment with RAxML, using the PROTCATLG model. Bootstrap support is displayed for branches supported by more than 50 bootstrap trees. Clades were collapsed to provide a more readable tree. The number of members of major taxonomic groups is presented in parentheses next to each collapsed clade. Misc represents miscellaneous groups with three or fewer representatives. Cyanobacteria are depicted in blue. The four major recognized clades of CA (A–D) are highlighted in different colours. An asterisk marks the localization of the ancestor of the cyanobacterial clade B carbonic anhydrase ancestor. The scale at the bottom of the tree represents the number of substitutions per site. The complete tree is depicted in the electronic supplementary material, figure S1. (Online version in colour.)

Figure 3.

Alignment and analysis of ancestors and extant sequences of the cyanobacterial group in clade B beta-carbonic anhydrase. The alignment is based on all 55 ancestors and 57 extant sequences. From top to bottom: the aligned sequences for the last common ancestor of the cyanobacterial sequences (node 67, shown with an asterisk in figure 2), and three extant sequences. Only the amino acids different from their respective consensus sequences below (black bar graph) are shown. The yellow bar graphs represent the conservation in the two groups. Columns of the alignment that had more gaps than sequences are not represented. The raw alignment is available at http://phylobot.com/38899544/. (Online version in colour.)

Figure 4.

Posterior probabilities of maximum-likelihood sequence residues, per position for the best (blue), second (orange) and third (grey) best residue, as reconstructed by phylobot.