Emily A. Seward and Steven Kelly
Genome Biology 2016, 17:226 (Published: 15 November 2016)
Abstract
Background
Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood.
Results
Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes.
Conclusions
Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.
See http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1087-9
Fig. 1
Phylogenetic trees of the parasites used in this study shaded according to their host and metabolic strategy. Green indicates plant parasites that obtain energy from carbohydrate catabolism (low nitrogen availability, L N ). Yellow indicates animal parasites that obtain energy from carbohydrate catabolism (medium nitrogen availability, M N ). Orange indicates animal parasites that obtain energy from amino acid and/or amino sugar catabolism (high nitrogen availability, H N )
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