Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition

Abstract

The new field of “stoichiogenomics” integrates evolution, ecology, and bioinformatics to reveal surprising patterns of differential usage of key elements (e.g., nitrogen, N) in proteins and nucleic acids. Because the canonical amino acids as well as nucleotides differ in element counts, natural selection due to limited element supplies might bias monomer usage to reduce element costs. For example, proteins that respond to N limitation in microbes use a lower proportion of N-rich amino acids, whereas proteome- and transcriptome-wide element contents differ significantly for plants as compared to animals, likely because of differential severity of element limitations. In this review, we show that with these findings, new directions for future investigations are emerging, particularly via the increasing availability of diverse meta-genomic and meta-transcriptomic data sets.

Physiological and Proteomic Analysis of Escherichia coli Iron-Limited Chemostat Growth

“…Gels were stained with blue silver (59), and spots were cut by hand. The gel pieces were destained (25 mM NH 4 To recover the peptides, 100 l of Nanopure water was added to the excised gel pieces after digestion and vortexed for 10 min, followed by 5 min in a sonication bath. This first extract was transferred to a new tube containing 10 l of extraction solvent (50% [vol/vol] acetonitrile, 5% [vol/vol] formic acid).…”

“…Nutrient-limited growth is fundamental to cellular biology, influencing (i) the elemental composition of microorganisms (4-7), (ii) the amino acid sequence of nutrient transporters (4,8), and (iii) the amino acid sequence of highly expressed proteins (9). Iron-limited growth is of special interest in medical and marine sciences, where it is central to bacterial pathogenesis and global nutrient cycling, respectively.…”

Can resource costs of polyploidy provide an advantage to sex?

“…For example, Elser et al (2011) provide evidence that some variation in amino-acid composition among taxa reflects selection for efficient use of limited nutrients. Similarly, Hessen et al (2010) suggest that genome streamlining could be favored under conditions of P scarcity, particularly if there is corresponding selection for rapid growth.…”

Biological Stoichiometry: The Elements at the Heart of Biological Interactions

“…Recent studies uncovered long-term evolutionary responses to element deprivations: N-deprived organisms react by substituting N-rich amino-acids by amino-acids with N-poor residues in their expressed proteins or by expressing shorter mRNAs (Grzymski & Dussaq 2011). They also show RNAs with more Npoor nucleotides (Elser et al 2011). As for DNA, since GC and AT pairs have almost the same N content, N limitation seems to have less effect.…”

“…As for DNA, since GC and AT pairs have almost the same N content, N limitation seems to have less effect. These advances on the links between elemental limitation and cell polymer composition lead to the coining of a new term: "stoichiogenomics" (Elser et al 2011).…”