Distinct trends in chemical composition of proteins from metagenomes in redox and salinity gradients

Abstract

Thermodynamic influences on the chemical compositions of proteins have remained enigmatic despite much work that demonstrates the impact of environmental conditions on amino acid frequencies. Here, we show that the dehydrating effect of salinity is apparent in protein sequences inferred from metagenomes and metatranscriptomes. The stoichiometric hydration state (n H 2 O ), derived from the number of water molecules in theoretical reactions to form proteins from a particular set of basis species (glutamine, glutamic acid, cysteine, O 2 , H 2 O), decreases along salinity gradients including the Baltic Sea, Amazon River and ocean plume, and other samples from freshwater and marine environments. Analysis of other metagenomic datasets shows that differences in carbon oxidation state, rather than stoichiometric hydration state, are a stronger indicator of redox gradients than salinity gradients. These compositional metrics can help to identify thermodynamic effects in the distribution of proteins along chemical gradients at scales from geologic systems to cells.

Water as a reactant in the differential expression of proteins in cancer

“…This finding might be linked with the less liquid-like state of the cytoplasm in 3D culture (64). These results are also congruent with metagenomes of particle-sized fractions compared to freeliving microbes in river and marine samples; the former, which are more likely to harbor multicellular communities, are associated with lower n H 2 O of the coded proteins (20). In addition, up-regulated proteins in 3D culture also tend to be more reduced (Table 2), which might be a reflection of the hypoxic conditions that develop in the interiors of spheroids (21,22,65).…”

“…This derivation, denoted "rQEC", is briefly described in the Materials and Methods; see Ref. 20 for more details and conceptual background.…”

“…S4 C-D), which calls into question the uniqueness of hydration state calculated using this method. This covariation is reduced in the rQEC derivation of stoichiometric hydration state (20), making it more useful to distinguish condition-specific trends of oxidation and hydration state in differentially expressed proteins.…”

“…Values of average oxidation state of carbon (Z C ) of amino acids (Table 1) were calculated from the chemical formulas of the amino acids (25,26). Values for Z C of proteins were computed by combining the amino acid compositions of proteins with Z C of amino acids and also weighting by carbon number (20).…”