Prokaryotic genome design is ruled by the mechanical properties and complexity of the DNA sequence

Abstract

Although we represent the genetic code using four letters, namely A, T, G, and C, it is a chemical entity with sequence-dependent physical properties and a spatial extent. In other words, it can be said that genetic information is compressed and recorded in the genomic DNA as a storage medium with a spatial spread. This study analyzed prokaryotic genomes in terms of their physical properties and complexity. The findings clearly indicated that a mathematic equation can be used to express the relationship between the length of a genome and the upper limit of its rigidity. Furthermore, many prokaryotes have been shown to maximize DNA complexity under various physical constraints. Here, this relationship between rigidity and complexity was found to be shaped like an entropy function. It was also clarified that codon usage tendencies are affected by the physical properties and complexity of the DNA sequence. Moreover, the analysis of codons encoding two consecutive synonymous amino acids suggests that many prokaryotic codon combinations tend to increase genomic DNA complexity. This study revealed the macro-level rules for packing genomic DNA into prokaryotic cells.