Nucleotide Composition Plots: A Key to Biological Insights

Important fundamental questions remain to be answered in biology, particularly concerning the coordination of many proteins and overall stability of living organisms. To address these questions, we clarify—by analogy with phase diagrams in materials science—that a nucleotide composition plot (NC-plot) for genomes can be regarded as a phase diagram of life. The NC-plot for a genome considerably deviates from a completely random composition, and it provides insights into the mechanism by which genomic order emerges from random mutations. Furthermore, an analysis of the NC-plot for all genes in a genome reveals relationships between nucleotide composition and various protein properties, including differences in evolutionary rates and distributions of protein folds. Finally, an analysis of the NC-plot for viral genomes suggests that both the coordination of proteins and stability of organisms are determined by genome processing systems (i.e., intracellular factors).