Relating digital information, thermodynamic stability, and classes of functional genes in E. coli

摘要

Tremendous efforts have been made to analyze and discern the digital information content of the DNA ever since the introduction of the Watson-Crick model, later fueled by the availability of genomic data. However, there is also an analog type of information which is related to the physicochemical properties of the DNA, manifested in structural and topological variations of the chromosome. Hence, investigating the relationship between digital information contained in the sequence of bases and the analog parameters associated with it is very important to the general understanding of the coding structure in the DNA. In this paper, we represented analog information by thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequence of the bacteria Escherichia coli (E. coli). Furthermore, the link to the broader classes of functional gene groups (anabolic, catabolic, aerobic, and anaerobic) is examined. In most regions of the genome, the Shannon and Gibbs entropies are anti-correlated. Around the terminus, there is an almost perfect anti-correlation with high Shannon and low Gibbs entropies, meaning that the sequence is more random and at the same time less stable. The other core finding is the very high similarity in the profiles of entropies and the distribution of anabolic genes.