Using thermodynamics to obtain geochemical information from genomes

Abstract

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH2) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH2 and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH2 values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia‐oxidizing archaea) occurs at a less‐reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.

Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution

“…For the purposes of illustration, we selected reference proteomes for five methanogen species ( Methanococcus vannielii , Methanococcus maripaludis , Methanococcus voltae , Methanobrevibacter smithii , and Methanofollis liminatans ) having a range of Z C from −0.220 for M. vannielii to −0.154 for M. liminatans (see Fig. 1 in reference 101 ). These species represent a diverse phylogeny, including both Class I and Class II methanogens, but they are all mesophiles with optimal growth temperatures of 30°C–40°C.…”

The Geochemical Potential for Metabolic Processes on the Sub-Neptune Exoplanet K2-18b

“…This is not to say that atmospheric chemistry cannot also produce key organic building blocks (Madhusudhan et al 2023b). The occurrence of hycean conditions would therefore have implications for the possible origin of life (Martin et al 2008) and how the environment may influence the composition of life (Dick et al 2023), as yet unknown on K2-18b. Notes.…”

chem16S: community-level chemical metrics for exploring genomic adaptation to environments

“…H, N, O, and S in the primary sequences of proteins). Protein Z tends to be lower in the genomes of methanogens that inhabit anoxic environments compared to those that are occasionally found in oxygenated environments ( Dick et al 2023 ). This suggests that geochemical relative stability models are applicable to genomic variation, but identifying the role of the environment is complicated by the cosmopolitan nature of many organisms.…”