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Biogeosciences An interactive open-access journal of the European Geosciences Union
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https://doi.org/10.5194/bg-2020-146
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-2020-146
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Submitted as: research article 15 May 2020

Submitted as: research article | 15 May 2020

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This preprint is currently under review for the journal BG.

Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences

Jeffrey M. Dick1,2, Miao Yu1, and Jingqiang Tan1 Jeffrey M. Dick et al.
  • 1Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
  • 2State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China

Abstract. Thermodynamic influences on the chemical compositions of proteins in nature have remained enigmatic despite much work that demonstrates the impact of environmental conditions on amino acid frequencies. Here, we present evidence that the dehydrating effect of salinity is detectable as chemical differences in protein sequences inferred from (1) metagenomes and metatranscriptomes in regional salinity gradients and (2) differential gene and protein expression in microbial cells under hyperosmotic stress. The stoichiometric hydration state (nH2O), derived from the number of water molecules in theoretical reactions to form proteins from a particular set of basis species (glutamine, glutamic acid, cysteine, O2, H2O), decreases along salinity gradients including the Baltic Sea and Amazon River and ocean plume and in particle-associated compared to free-living fractions. However, the proposed metric does not behave as expected for hypersaline environments. Analysis of data compiled for hyperosmotic stress experiments under controlled laboratory conditions shows that differentially expressed proteins, as well as proteins coded by differentially expressed transcripts, are on average shifted toward lower nH2O. Notably, the dehydration effect is stronger for most organic solutes compared to NaCl. This new method of compositional analysis can be used to identify possible thermodynamic effects in the distribution of proteins along chemical gradients at a range of scales from biofilms to oceans.

Jeffrey M. Dick et al.

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Jeffrey M. Dick et al.

Model code and software

canprot 1.0.0 J. M. Dick https://doi.org/10.5281/zenodo.3820154

JMDplots 1.2.2 J. M. Dick https://doi.org/10.5281/zenodo.3824121

Jeffrey M. Dick et al.

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Short summary
Differences of salt concentration are widespread in ecosystems. Using protein sequences predicted from DNA of microbial communities, we found that the number of H2O in chemical reactions between proteins tracks environmental salinity gradients. Datasets for proteins in experiments with salt or organic solutes show a similar effect. These relationships between salt concentration and the chemical compositions of proteins demonstrate the impact of geochemical conditions on microbial evolution.
Differences of salt concentration are widespread in ecosystems. Using protein sequences...
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