Research Article

Resource conservation manifests in the genetic code

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Science  06 Nov 2020:
Vol. 370, Issue 6517, pp. 683-687
DOI: 10.1126/science.aaz9642

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Maximizing elements for your genome

The accumulation of mutations is typically limited by selective parameters. One such parameter is the elements needed to build proteins and molecules to maintain cells. Examining the underlying carbon, oxygen, and nitrogen content for different amino acids, Shenhav et al. examined the selective pressure resulting from nutrient limitation (see the Perspective by Polz and Cordero). The authors identified “resource-driven” selection as a purifying selective force associated with environmental nutrient availability, particularly nitrogen, and determined the impact of mutations on the organismal nutritional budget. From this constraint, the authors have proposed that the structure of the genetic code across organisms reflects the mutational impact on elemental resources.

Science, this issue p. 683; see also p. 655

Abstract

Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. This robustness generalizes to codon choices from multiple taxa across all domains of life, including the human genome.

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